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Working Group and next Advances-Fringe Tomo-Week

18 December 2019 is the Xmas Working Group session with seminar booked: Harwell Campus and university of Manchester.

  • We will have a CIL (Core Imaging Library) hackathon at the Harewll Campus on 16-18 December
  • Working Group 10:30am Coffee arrives; 11am-12noon and lunch talk at 12noon-1pm
  • Seminar 18 December 2019 12noon

8-12 June 2020 Advances-Fring an Alan Turing Institute Summer School.

ATI_logo_black_W1024px.jpg

 

The "Fringe" Meeting Monday 10 June 2019

Invitation to the Fringe meeting: short informal presentations focusing on creating an Intelligent Framework: Pros and Cons of AI/ML in the Computed Tomography pipeline with support and sponsorship from The Alan Turing Institute

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"Wedged as we are between two eternities of idleness, there is no excuse for being idle now" Anthony Burgess
 CCPi links and work carried out within SCD/STFC and related parties. This wiki is a community site to update on administrative (EPSRC / SCD) targets and discussion points.

The CCPi network was established in 2012 to support the emerging UK tomography community with a toolbox of algorithms to increase the quality and level of information that can be extracted by computed tomography. There are four major open source software parts supported: pre-processing techniques for image calibration and noise reduction; reconstruction techniques to create a 3D volume data set from projections; segmentation/quantification techniques that can extract relevant objective values from these 3D volumes; and a software framework development to enable the exploitation across a wide range of imaging devices.

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    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
  • Finish at 5pm
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  Specialist HPL-CCPi meeting 4:30pm-5:15pm
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  Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
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Video Conf link - Physically based RAL - Harwell Campus
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Video Conf link - Linkedin poster winners:

https://www.linkedin.com/feed/update/urn%3Ali%3Aactivity%3A6544494105857179648/?midToken=AQEwjhmm2bWdBQ&trk=eml-email_notification_single_mentioned_you_in_this_01-notifications-1-hero~card~feed&trkEmail=eml-email_notification_single_mentioned_you_in_this_01-notifications-1-hero~card~feed-null-b6fxx~jwszm3qr~dq-null-voyagerOffline

 

Past Topics:

2019 Fringe Pros and Cons of AI/ML in the CT pipeline

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      • Hackathon #4
      • Update on CIL Core Imaging Library
      • Update on multispectral Flagship grant
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  • 12noon-12:45pm Lunch-and-Learn Specialist Talk - ALL invited
    • Joe Kelleher on EnginX
  • 12:45pm-1:45pm Lunch
  • 1:45pm-4:30pm The Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
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  • The Fringe Agenda
    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (!JT@STFC, WK@UoWarwick)
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    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
  • Finish at 5pm
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Wifi: visitors have to fill this form https://visitorwifi.stfc.ac.uk

Video Conference Link: https://ukri.zoom.us/j/352946090

 Specialist HPL-CCPi meeting 4:30pm-5:15pm

Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

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Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

  1. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  2. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
 
  1. * Jingyi Mo University College London ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’
  2. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre AI-Vision
  3. * Wilfrid Kendall, Warwick University
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  Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk
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  • To Be Confirmed neaer the date
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2016 Fringe Do we really need Synchrotrons
TUESDAY 11 June 2019
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
  WEDNESDAY 12 and THURSDAY 13 June 2019
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 CCP hackathn #4 - 12-13 June 2019 after the Workshops in RAL; a topic will be inviting the Diamond Light Source developers to see how to mix the CCPi software and Flagship python framework system, more effectively with savu.

Last year's event, 2018

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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
 
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
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  Register here:
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  Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
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    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
  2. A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
 
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
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  • to hand-hold transfer-code development for "the Astra Toolbox for CT reconstructions of data from the Nikon 225" for Llion Evans
  • for hackathon in April 2019 (see below)
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  • for https://www.turing.ac.uk/events/data-centric-materials-science-and-engineering involving advertisement and attendance
  • for http://dxct.hud.ac.uk/ in June 2019 - proposed support for student attendance; and CCPi stand to be made available
  • for https://mecheng.ucl.ac.uk/imagingbiopro/ only advertisement
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  • LoS New Investigator Award EPSRC proposal 'Limited Data X-ray CT for Measurement'
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  • for Fringe event in June 2019 prior to Advances in Xray Imaging http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiTomo
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  • ...
  • Other Links: ToScA UK need contacting
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  3. CIL Build-and-Test automation (from Tomas Kulhanek)
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  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
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  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`

4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm

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  • Atlas Visualisation Facility at Harwell Campus (RAL) and
  • ... ICAM building at University of Manchester and
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  • ... by video-conference through https://ukri-stfc.zoom.us/j/418481169
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  For catering please email if you wish to attend: martin.turner@manchester.ac.uk
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  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on code C01
  • SCARF18 - should be open for SCD staff
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  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
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  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
  Accepted (11): Mark Basham, Mark Williams, M Soleimani, Martin Turner, Martyn Winn, Parmesh Gajar, Jay Warnett, Phil Withers, Edo Pasca, Evangelos (Vaggelis) Papoutsellis, Bob Cernik, Bill Lionheart
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  • CCPi Fellowships approved and visits: Brian Bay x2 as well as summer visitors (mainly at dXCT).
  • Grants submitted with Letters of Support from CCPi: WMG is approved.
  • Joint CCP hackathon - workshops/events on code integration
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  CCPi conferences and workshops: Summer 2018
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  • ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
  2. CIL-Core development: linking with Flagship software
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 Papers etc:

  • TomoPhantom software and paper:https://github.com/dkazanc/TomoPhantom
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  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
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  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop
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  • Website and email list (review by EP/MT)
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
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  • Beamtime; IMAT February 2019

Points Raised with more details: from November 2017 meeting:

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  Other items:
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  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

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 Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 
  1. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  2. Are you involved in any eCSE projects (please provide details)? No
  3. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
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  Other points:
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  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)
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  1. Elizabeth.Surrey@
  2. rob.akers@
  3. daniel.pooley@
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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

 
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
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    • distibution jiscmail lists
    • website content etc
    • HPC: SCARF18, Archer access.
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  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
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  • AOB
    • Location for next WG at RAL
    • GDPR issues
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  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

 
Exec Meeting Agenda (Nov 2017 - Mar 2018) 29 March 2018, 9:30am "To discuss the new coding and outcomes from the Core and Flagship environment"
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  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
  - dimension XCT: speakers so far (plus one) July 2018 ACTION Requested funds for travel for students on usual basis
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  • Software to generate 2D-4D analytical phantoms and their Radon transforms for image processing
  • Paper submitted to Software X
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  Extra:
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  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
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    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
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  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
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  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
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  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
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  Training / Seminar:

  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
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  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
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  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
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  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
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  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
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  • 6 December 2017 - Flagship-IMAT meeting in RAL to update on progress.
  • Flagship-CIL code-sprint 5-8 March 2018 - plan to repeat.
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  • 29 January - 9 February 2018 ISO / TC 213 WG10 standards meeting at BSI (389 Chiswick High Road, London E4 4AL). In the first week, Monday and Tuesday 9am-12noon XCT general topics; and Wednesday 3pm-5:30pm & Friday 9am-11:30am ISO Cttee deliberations.

Appendix A: details of events November 2017 - May 2018

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  Agenda 10:30am coffee - meeting 11am-2pm including Lunch
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
  Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
Line: 903 to 907
 
  • (10 mins) actions + further discussion
  • AOB
Changed:
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
 
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
Line: 912 to 916
 
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
Changed:
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  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
>
>
 
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
Changed:
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  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
>
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  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
Line: 954 to 958
 
  • MT to write a summary for SCD newsletter on CCPi activities
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day
Changed:
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
>
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
 

CCPi Flagship session: 2pm-3:30pm

Items:

  • ISIS IMAT Phantom data acquisition process
Changed:
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  • Flagship items from grant and last June meeting: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiFlagship
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>
 
  • Future meetings and integration
Changed:
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  • Additions to website: https://www.ccpi.ac.uk/Flagship
>
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  • ...

Appendix A: details of events June 2016 - October 2017

Line: 1032 to 1036
  Atlas Visualisation Facility: Monday 12 June 2017 - registration at:
Changed:
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  • Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-preadvances-in-x-ray-imaging-tickets-32623491742
>
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Changed:
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There will be video conferencing available: https://bluejeans.com/576183356/
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There will be video conferencing available: https://bluejeans.com/576183356/
  Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm

  • Approval of past six months activities (SN)
Changed:
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    • approval of secretariat roles (http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole)
>
>
 
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
Line: 1062 to 1066
 
    • Image / vidoe archive on website inc Flagship pics
    • ...
Changed:
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
  Combined Presentation: CCPiJune2017WG_c.pdf
Line: 1091 to 1095
 Links: current EPSRC equipment Roadmap:
Changed:
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
 

Networking and Funding Activities: December 2016 - May 2017

Line: 1099 to 1103
 
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
Changed:
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
>
>
    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
 
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
  • Three exhibitions:
    • 4-18 November 2016 Supercomputing Videos and interactive volume visualisation system at Hartree Centre stand #1137:
Line: 1111 to 1115
 
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
    • Workshop on SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
Changed:
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    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
>
>
 
  • BSI Standards involvement:
    • 11 January 2017 BSI standards meeting of the XCT panel (TDW/4/4/1)
Changed:
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    • XCT user meeting events@npl.co.uk 8 March 2017 https://www.eventbrite.co.uk/e/xct-user-meeting-registration-31024486073
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  • Developers' days:
    • 20 March 2017 pre-Flagship meeting at RAL and 11 May 2017 telephone-conf update.
  • Papers etc:
Line: 1123 to 1127
  Continual CCPi support for the three annual events:
Changed:
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
>
>
  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
 
  1. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific Advancement symposium addressing hard and soft tissue imaging, understanding materials in 3D, recent advances in hardware and software, and a broad range of applications in tomography www.rms.org.uk/tosca2017

Coding Milestones : December 2016 - May 2017

Line: 1197 to 1201
 
  • Proposed Summer school in Tomo at Bath 2017
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)
  • Support for "short course /workshop as part of EGU2017. The subject would be automation of image analysis from large datasets using freeware. Probably I would focus on using imageJ."Jose Godinho
Changed:
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  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf
>
>
 
CCPi Executive Summary, last six months: June 2016-November 2016

Line: 1215 to 1219
  Website refreshed and data archives in use (zenodo and dropbox for business are now available).
Changed:
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https://www.ccpi.ac.uk/
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https://www.ccpi.ac.uk/
 
Changed:
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https://zenodo.org/communities/ccpi/?page=1&size=20
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https://zenodo.org/communities/ccpi/?page=1&size=20
 

Coding Milestones from the core SLA funds: To be discussed.

Current set for 2016-2017 are:

Line: 1234 to 1238
 
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
Changed:
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
>
>
We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
  Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.
Line: 1255 to 1259
 
  • ... link to S-J C and MT for sections
  • CECAM event at DL – on Drishti / Avizo
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
Changed:
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  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
>
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  • EU COST grant: application for 2017

Proposals (speculative):

Line: 1285 to 1289
 
  • Logos on stickers and mugs
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.
Changed:
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 

Appendix B – details of events June 2016-November 2016

Line: 1308 to 1312
 
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU:https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
Changed:
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  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
>
>
 
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Line: 1319 to 1323
 
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
Changed:
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  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
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  Training ; six advertised:
Line: 1476 to 1480
  - Infrastructure:
Changed:
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
  Update with touchscreen items (link to ICAL Russell Garwood).
Line: 1529 to 1533
 
  1. memory management to be improved esp for 3D data
  2. rotation based optimisation
Changed:
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
>
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
  slicerRT is more possibly more about the "quantification" of the processed data while the stir project is more about the reconstruction methods.
Line: 1582 to 1586
 
  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
Changed:
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
>
>
 
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.
Line: 1768 to 1772
  Deliverables produced:
Changed:
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
  “4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
Line: 1810 to 1814
 

Reconstruction Toolkit:

Changed:
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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
  Core Workplan: 0.5 FTE

Items from discussion:

Changed:
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>
>

 
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
Line: 1830 to 1834
  Co-ordinate collaboration with CCPASEArch; ASEArch activites include work with Evgueni Ovtchinnikov commencing 1 April 2014: This work is ASEArch related and is specific to that cost code. The work involves numberical methods, to apply a multigrid solution to improve the issues caused by a gradient based regulisation coefficient, as applied to an iterative CGM (Conjugate Gradient Method) that is coordinated by the CCPi Flagship fellow, Daniil Kazantsev. These activities are in their very early stages to improve the convergence of the algorithm but requires data analysis.
Changed:
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
 
Changed:
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
>
>
- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
 

Quantification Toolkit:

The quantification toolkit involved integration of code within Avizo, VolView and possibly ImageJ (and possibly Drishti); (Note now ParaView does volume visualisation this is an option as well).

Changed:
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
  Core Workplan: 0.5 FTE

Items from discussion:

Changed:
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>
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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
Line: 1864 to 1868
  Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.
Changed:
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
>
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
 
Changed:
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
>
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
  Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
Line: 1883 to 1887
  Papers etc.:
Changed:
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
>
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
  Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.
Line: 1903 to 1907
  CCPi monitors/promotes various training courses including
Changed:
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  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
>
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  • 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data. (Day 1: Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) (Day 2: Introduction to Avizo Fire workshop (quantification), Analysis of inter-connected structures using Avizo and ImageJ)
  • Thursday 8 May 2014 - Aviso training - specialist session
  • June - week long session at University of Manchester
Line: 1915 to 1919
  Deliverables - Reconstruction and Quantification through the CCPi community
Changed:
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Main website is at: http://www.ccpi.ac.uk/
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Main website is at: http://www.ccpi.ac.uk/
 

End of Project Targets

Revision 20805 Jun 2019 - MartinTurner

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META TOPICPARENT name="WebHome"

CCPi Tomographic Imaging

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  ATI_logo_black_W1024px.jpg
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Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
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Registation for the 2019 Fringe event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
  The event will focus on essential, and past, AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.

MONDAY 10 June 2019: In main Pickavance Theatre (Harwell Campus - RAL)

  • 10am-1030am Coffee and biscuits
Changed:
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  • 10:30am CCPi Working Group event in AVF (Harwell Campus, Atlas Building)
>
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  • 10:30am CCPi Working Group event in Pickavance (R22) (Harwell Campus, Atlas Building)
 
    • Agenda:
      • Network Funds requested and short-term fellowships
      • LoS (Letters of Support) requests
Line: 28 to 28
 
      • Hackathon #4
      • Update on CIL Core Imaging Library
      • Update on multispectral Flagship grant
Changed:
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    • Register (just for the Working Group) at: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u
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  • 12noon-12:45pm Lunch-and-Learn Specialist Talk - ALL invited
    • Joe Kelleher on EnginX
  • 12:45pm-1:45pm Lunch
Changed:
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  • 1:45pm-4:30pm The Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
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  • 1:45pm-4:30pm The Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
 
Line: 42 to 42
 
    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
  • Finish at 5pm
Changed:
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Specialist HPL-CCPi meeting 4:30pm-5:30pm.
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Specialist HPL-CCPi meeting 4:30pm-5:15pm
  Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

Direct to dinner - DR@MINES,

Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

Deleted:
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  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests'
 
  1. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  2. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
  3. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
Line: 58 to 57
 
  1. * Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
  2. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  3. Dan Bull, University of Southampton ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’
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  1. * possible; Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
  2. ...
>
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  1. Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
  2. David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests'
 
  1. with 3DM sponsorship.

Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk

Line: 67 to 66
 Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991

Video Conf link - Physically based RAL - Harwell Campus

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  • Join Zoom Meeting: https://ukri.zoom.us/j/352946090
  • One tap mobile +442036950088,,352946090# United Kingdom +442039663809,,352946090# United Kingdom
  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
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  • To Be Confirmed neaer the date
 

Past Topics:

2019 Fringe Pros and Cons of AI/ML in the CT pipeline

Revision 20704 Jun 2019 - MartinTurner

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META TOPICPARENT name="WebHome"

CCPi Tomographic Imaging

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    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
>
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    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
 
    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (!JT@STFC, WK@UoWarwick)
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    • 2:20pm-3:00pm Talks by (AH@CWI) and key individuals 3x10mins (DR@MINES, MB@DLS, !XY@DESY)
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    • 2:20pm-3:00pm Talks by (AH@CWI) and key individuals 3x10mins (MB@DLS, !XY@DESY)
 
    • 3:00pm-3:30pm Coffee and Muffins
    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
  • Finish at 5pm
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 Specialist HPL-CCPi meeting 4:30pm-5:30pm.

Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

Added:
>
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Direct to dinner - DR@MINES,
 

Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests'
  2. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'

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CCPi Tomographic Imaging

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    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (JT@STFC, WK@UoWarwick)
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    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (!JT@STFC, WK@UoWarwick)
 
    • 2:20pm-3:00pm Talks by (AH@CWI) and key individuals 3x10mins (DR@MINES, MB@DLS, !XY@DESY)
    • 3:00pm-3:30pm Coffee and Muffins
    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers

Revision 20503 Jun 2019 - MartinTurner

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CCPi Tomographic Imaging

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      • Hackathon #4
      • Update on CIL Core Imaging Library
      • Update on multispectral Flagship grant
Changed:
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    • Register (just for the Working Group) at: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u
>
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    • Register (just for the Working Group) at: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u
 
  • 12noon-12:45pm Lunch-and-Learn Specialist Talk - ALL invited
    • Joe Kelleher on EnginX
  • 12:45pm-1:45pm Lunch
  • 1:45pm-4:30pm The Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
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  • The Fringe Agenda
    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (JT@STFC, WK@UoWarwick)
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 Specialist HPL-CCPi meeting 4:30pm-5:30pm.

Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

Changed:
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<

Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

>
>

Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

 
  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests'
  2. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
Changed:
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
 
  1. * Jingyi Mo University College London ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’
  2. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre AI-Vision
  3. * Wilfrid Kendall, Warwick University
Line: 62 to 62
  Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk
Changed:
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Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
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Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
  Video Conf link - Physically based RAL - Harwell Campus
Changed:
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  • Join Zoom Meeting: https://ukri.zoom.us/j/352946090
>
>
  • Join Zoom Meeting: https://ukri.zoom.us/j/352946090
 
  • One tap mobile +442036950088,,352946090# United Kingdom +442039663809,,352946090# United Kingdom
Changed:
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  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
>
>
  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
 

Past Topics:

2019 Fringe Pros and Cons of AI/ML in the CT pipeline
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2018 Fringe Cross reconstruction Software Sharing techniques
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
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 TUESDAY 11 June 2019
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
>
>
4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
  WEDNESDAY 12 and THURSDAY 13 June 2019
Line: 88 to 87
 CCP hackathn #4 - 12-13 June 2019 after the Workshops in RAL; a topic will be inviting the Diamond Light Source developers to see how to mix the CCPi software and Flagship python framework system, more effectively with savu.

Last year's event, 2018

Changed:
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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
 
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
  pano57w.jpg
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  WP_20180614_002plus_w.jpg
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
  p20180614_151248_bp40w.jpg
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 p20180614_193711_13p40w.jpg

<a name="WorkingGroup"></a>

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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

>
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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
Line: 138 to 137
 6. New data storage area path is \\nasr.man.ac.uk\epsrss$\snapped\replicated\CCPi_RTMCT

7. Haching Code results/updates ... "CCPi. We had a version of your code on CCPi forge but I didn't do anything before they closed it. I am thinking we should dig it out again and with some help from Parmesh get some demo scripts for using with Nikon. Parmesh is also working on how to access the Zeiss system (I think) so we could do that too" to henry and gemma, BL

Added:
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Planning for d-XCT 2020 roles:
  • website
  • registration
  • room booking
  • tutorial coordination
  • speaker coordination
  • exhibition and sponsors
  • registration desk and accommodation advice
  • ...
 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Register here:

Changed:
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https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
  Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
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    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
  2. A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
Changed:
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
>
>
    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
 
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
Line: 170 to 180
 
  • to hand-hold transfer-code development for "the Astra Toolbox for CT reconstructions of data from the Nikon 225" for Llion Evans
  • for hackathon in April 2019 (see below)
Changed:
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  • for https://www.turing.ac.uk/events/data-centric-materials-science-and-engineering involving advertisement and attendance
  • for http://dxct.hud.ac.uk/ in June 2019 - proposed support for student attendance; and CCPi stand to be made available
  • for https://mecheng.ucl.ac.uk/imagingbiopro/ only advertisement
>
>
  • for https://www.turing.ac.uk/events/data-centric-materials-science-and-engineering involving advertisement and attendance
  • for http://dxct.hud.ac.uk/ in June 2019 - proposed support for student attendance; and CCPi stand to be made available
  • for https://mecheng.ucl.ac.uk/imagingbiopro/ only advertisement
 
  • LoS New Investigator Award EPSRC proposal 'Limited Data X-ray CT for Measurement'
Changed:
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  • for Fringe event in June 2019 prior to Advances in Xray Imaging http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiTomo
>
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  • for Fringe event in June 2019 prior to Advances in Xray Imaging http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiTomo
 
  • ...
  • Other Links: ToScA UK need contacting
Line: 194 to 204
  3. CIL Build-and-Test automation (from Tomas Kulhanek)
Changed:
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  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
>
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  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
 
  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`

4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm

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  • Atlas Visualisation Facility at Harwell Campus (RAL) and
  • ... ICAM building at University of Manchester and
Changed:
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  • ... by video-conference through https://ukri-stfc.zoom.us/j/418481169
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  • ... by video-conference through https://ukri-stfc.zoom.us/j/418481169
  For catering please email if you wish to attend: martin.turner@manchester.ac.uk
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  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on code C01
  • SCARF18 - should be open for SCD staff
Changed:
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  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
>
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  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
  Accepted (11): Mark Basham, Mark Williams, M Soleimani, Martin Turner, Martyn Winn, Parmesh Gajar, Jay Warnett, Phil Withers, Edo Pasca, Evangelos (Vaggelis) Papoutsellis, Bob Cernik, Bill Lionheart
Line: 428 to 438
 
  • CCPi Fellowships approved and visits: Brian Bay x2 as well as summer visitors (mainly at dXCT).
  • Grants submitted with Letters of Support from CCPi: WMG is approved.
  • Joint CCP hackathon - workshops/events on code integration
Changed:
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  • Lunch-and-Learn and Show-and-Tell events: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars
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  • Lunch-and-Learn and Show-and-Tell events: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars
  CCPi conferences and workshops: Summer 2018
Line: 438 to 448
 
  • ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
Changed:
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
>
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
  2. CIL-Core development: linking with Flagship software
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 Papers etc:

  • TomoPhantom software and paper:https://github.com/dkazanc/TomoPhantom
Changed:
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  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
>
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  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
 
  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop
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  • Website and email list (review by EP/MT)
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
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  • Beamtime; 4 September 2018 Advanced Radiotherapy https://www.birmingham.ac.uk/research/activity/nuclear/about-us/Facilities.aspx with Swansea
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  • Beamtime; 4 September 2018 Advanced Radiotherapy https://www.birmingham.ac.uk/research/activity/nuclear/about-us/Facilities.aspx with Swansea
 
  • Beamtime; IMAT February 2019

Points Raised with more details: from November 2017 meeting:

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  Other items:
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  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
>
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  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
 
  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

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 Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
Changed:
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
>
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 
  1. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  2. Are you involved in any eCSE projects (please provide details)? No
  3. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
Line: 545 to 555
  Other points:
Changed:
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  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
>
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  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
 
  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)
Line: 601 to 611
 
  1. Elizabeth.Surrey@
  2. rob.akers@
  3. daniel.pooley@
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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

>
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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

 
Changed:
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
>
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
Line: 644 to 654
 
    • distibution jiscmail lists
    • website content etc
    • HPC: SCARF18, Archer access.
Changed:
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  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
>
>
  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
 
  • AOB
    • Location for next WG at RAL
    • GDPR issues
Line: 672 to 682
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
Changed:
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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

>
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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

 
Exec Meeting Agenda (Nov 2017 - Mar 2018) 29 March 2018, 9:30am "To discuss the new coding and outcomes from the Core and Flagship environment"
Line: 694 to 704
 
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
Changed:
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
>
>
- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
  - dimension XCT: speakers so far (plus one) July 2018 ACTION Requested funds for travel for students on usual basis
Line: 748 to 758
 
  • Software to generate 2D-4D analytical phantoms and their Radon transforms for image processing
  • Paper submitted to Software X
Changed:
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  • Code available at https://github.com/dkazanc/TomoPhantom
>
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  • Code available at https://github.com/dkazanc/TomoPhantom
 
Changed:
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
>
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  Extra:
Line: 762 to 772
 
  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
Changed:
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    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
>
>
    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
 
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
Line: 778 to 788
 
  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
Changed:
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  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
>
>
  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
  Training / Seminar:

  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
Changed:
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  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
>
>
  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
 
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
Changed:
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  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
>
>
  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
 
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
Line: 829 to 839
 
  • 6 December 2017 - Flagship-IMAT meeting in RAL to update on progress.
  • Flagship-CIL code-sprint 5-8 March 2018 - plan to repeat.
Changed:
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  • 12 December 2017 EPSRC XCT Tomography Equipment Roadmap, Townhall Meeting (Manchester) https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
>
>
  • 12 December 2017 EPSRC XCT Tomography Equipment Roadmap, Townhall Meeting (Manchester) https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
 
  • 29 January - 9 February 2018 ISO / TC 213 WG10 standards meeting at BSI (389 Chiswick High Road, London E4 4AL). In the first week, Monday and Tuesday 9am-12noon XCT general topics; and Wednesday 3pm-5:30pm & Friday 9am-11:30am ISO Cttee deliberations.

Appendix A: details of events November 2017 - May 2018

Line: 854 to 864
  Agenda 10:30am coffee - meeting 11am-2pm including Lunch
Changed:
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
  Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
Line: 894 to 904
 
  • (10 mins) actions + further discussion
  • AOB
Changed:
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
 
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
Line: 903 to 913
 
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
Changed:
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  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
>
>
  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
 
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
Changed:
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  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
>
>
  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
 
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
Line: 945 to 955
 
  • MT to write a summary for SCD newsletter on CCPi activities
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day
Changed:
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
>
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
 

CCPi Flagship session: 2pm-3:30pm

Items:

  • ISIS IMAT Phantom data acquisition process
Changed:
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  • Flagship items from grant and last June meeting: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiFlagship
>
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  • Flagship items from grant and last June meeting: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiFlagship
 
  • Future meetings and integration
Changed:
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  • Additions to website: https://www.ccpi.ac.uk/Flagship
>
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  • Additions to website: https://www.ccpi.ac.uk/Flagship
 
  • ...

Appendix A: details of events June 2016 - October 2017

Line: 1023 to 1033
  Atlas Visualisation Facility: Monday 12 June 2017 - registration at:
Changed:
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  • Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-preadvances-in-x-ray-imaging-tickets-32623491742
>
>
  • Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-preadvances-in-x-ray-imaging-tickets-32623491742
 
Changed:
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There will be video conferencing available: https://bluejeans.com/576183356/
>
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There will be video conferencing available: https://bluejeans.com/576183356/
  Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm

  • Approval of past six months activities (SN)
Changed:
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    • approval of secretariat roles (http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole)
>
>
    • approval of secretariat roles (http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole)
 
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
Line: 1053 to 1063
 
    • Image / vidoe archive on website inc Flagship pics
    • ...
Changed:
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
>
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
  Combined Presentation: CCPiJune2017WG_c.pdf
Line: 1082 to 1092
 Links: current EPSRC equipment Roadmap:
Changed:
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
 

Networking and Funding Activities: December 2016 - May 2017

Line: 1090 to 1100
 
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
Changed:
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
>
>
    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
 
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
  • Three exhibitions:
    • 4-18 November 2016 Supercomputing Videos and interactive volume visualisation system at Hartree Centre stand #1137:
Line: 1102 to 1112
 
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
    • Workshop on SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
Changed:
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    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
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>
    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
 
  • BSI Standards involvement:
    • 11 January 2017 BSI standards meeting of the XCT panel (TDW/4/4/1)
Changed:
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    • XCT user meeting events@npl.co.uk 8 March 2017 https://www.eventbrite.co.uk/e/xct-user-meeting-registration-31024486073
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    • XCT user meeting events@npl.co.uk 8 March 2017 https://www.eventbrite.co.uk/e/xct-user-meeting-registration-31024486073
 
  • Developers' days:
    • 20 March 2017 pre-Flagship meeting at RAL and 11 May 2017 telephone-conf update.
  • Papers etc:
Line: 1114 to 1124
  Continual CCPi support for the three annual events:
Changed:
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
 
  1. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific Advancement symposium addressing hard and soft tissue imaging, understanding materials in 3D, recent advances in hardware and software, and a broad range of applications in tomography www.rms.org.uk/tosca2017

Coding Milestones : December 2016 - May 2017

Line: 1188 to 1198
 
  • Proposed Summer school in Tomo at Bath 2017
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)
  • Support for "short course /workshop as part of EGU2017. The subject would be automation of image analysis from large datasets using freeware. Probably I would focus on using imageJ."Jose Godinho
Changed:
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  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf
>
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  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf
 
CCPi Executive Summary, last six months: June 2016-November 2016

Line: 1206 to 1216
  Website refreshed and data archives in use (zenodo and dropbox for business are now available).
Changed:
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https://www.ccpi.ac.uk/
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https://www.ccpi.ac.uk/
 
Changed:
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https://zenodo.org/communities/ccpi/?page=1&size=20
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https://zenodo.org/communities/ccpi/?page=1&size=20
 

Coding Milestones from the core SLA funds: To be discussed.

Current set for 2016-2017 are:

Line: 1225 to 1235
 
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
Changed:
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
>
>
We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
  Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.
Line: 1246 to 1256
 
  • ... link to S-J C and MT for sections
  • CECAM event at DL – on Drishti / Avizo
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
Changed:
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  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
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  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
 
  • EU COST grant: application for 2017

Proposals (speculative):

Line: 1276 to 1286
 
  • Logos on stickers and mugs
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.
Changed:
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 

Appendix B – details of events June 2016-November 2016

Line: 1299 to 1309
 
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU:https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
Changed:
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  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
>
>
  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
 
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Line: 1310 to 1320
 
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
Changed:
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  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
>
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  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
  Training ; six advertised:
Line: 1467 to 1477
  - Infrastructure:
Changed:
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
>
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
  Update with touchscreen items (link to ICAL Russell Garwood).
Line: 1520 to 1530
 
  1. memory management to be improved esp for 3D data
  2. rotation based optimisation
Changed:
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
>
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
  slicerRT is more possibly more about the "quantification" of the processed data while the stir project is more about the reconstruction methods.
Line: 1573 to 1583
 
  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
Changed:
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
>
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
 
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.
Line: 1759 to 1769
  Deliverables produced:
Changed:
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
  “4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
Line: 1801 to 1811
 

Reconstruction Toolkit:

Changed:
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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
  Core Workplan: 0.5 FTE

Items from discussion:

Changed:
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>
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  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
Line: 1821 to 1831
  Co-ordinate collaboration with CCPASEArch; ASEArch activites include work with Evgueni Ovtchinnikov commencing 1 April 2014: This work is ASEArch related and is specific to that cost code. The work involves numberical methods, to apply a multigrid solution to improve the issues caused by a gradient based regulisation coefficient, as applied to an iterative CGM (Conjugate Gradient Method) that is coordinated by the CCPi Flagship fellow, Daniil Kazantsev. These activities are in their very early stages to improve the convergence of the algorithm but requires data analysis.
Changed:
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
 
Changed:
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
 

Quantification Toolkit:

The quantification toolkit involved integration of code within Avizo, VolView and possibly ImageJ (and possibly Drishti); (Note now ParaView does volume visualisation this is an option as well).

Changed:
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
  Core Workplan: 0.5 FTE

Items from discussion:

Changed:
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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
Line: 1855 to 1865
  Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.
Changed:
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
>
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
 
Changed:
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
>
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
  Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
Line: 1874 to 1884
  Papers etc.:
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
>
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
  Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.
Line: 1894 to 1904
  CCPi monitors/promotes various training courses including
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  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
>
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  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
 
  • 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data. (Day 1: Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) (Day 2: Introduction to Avizo Fire workshop (quantification), Analysis of inter-connected structures using Avizo and ImageJ)
  • Thursday 8 May 2014 - Aviso training - specialist session
  • June - week long session at University of Manchester
Line: 1906 to 1916
  Deliverables - Reconstruction and Quantification through the CCPi community
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Main website is at: http://www.ccpi.ac.uk/
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Main website is at: http://www.ccpi.ac.uk/
 

End of Project Targets

Revision 20431 May 2019 - MartinTurner

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    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
  • Finish at 5pm
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Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

Past Topics:

>
>
Specialist HPL-CCPi meeting 4:30pm-5:30pm.
 
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2019 Fringe Pros and Cons of AI/ML in the CT pipeline
2018 Fringe Cross reconstruction Software Sharing techniques
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:
>
>
Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

 
  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests'
  2. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
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  • Join Zoom Meeting: https://ukri.zoom.us/j/352946090
  • One tap mobile +442036950088,,352946090# United Kingdom +442039663809,,352946090# United Kingdom
  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
Added:
>
>

Past Topics:

2019 Fringe Pros and Cons of AI/ML in the CT pipeline
2018 Fringe Cross reconstruction Software Sharing techniques
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
  TUESDAY 11 June 2019

Revision 20330 May 2019 - MartinTurner

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CCPi Tomographic Imaging

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  The event will focus on essential, and past, AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.
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MONDAY 10 June 2019: In main Piccavance Theatry (Harwell - RAL)
>
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MONDAY 10 June 2019: In main Pickavance Theatre (Harwell Campus - RAL)
 
  • 10am-1030am Coffee and biscuits
  • 10:30am CCPi Working Group event in AVF (Harwell Campus, Atlas Building)
    • Agenda:

Revision 20230 May 2019 - MartinTurner

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CCPi Tomographic Imaging

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    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (JT@STFC, WK@UoWarwick)
    • 2:20pm-3:00pm Talks by (AH@CWI) and key individuals 3x10mins (DR@MINES, MB@DLS, XY@DESY)
>
>
    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (JT@STFC, WK@UoWarwick)
    • 2:20pm-3:00pm Talks by (AH@CWI) and key individuals 3x10mins (DR@MINES, MB@DLS, !XY@DESY)
 
    • 3:00pm-3:30pm Coffee and Muffins
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>
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    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
 
  • Finish at 5pm

Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.

Revision 20129 May 2019 - MartinTurner

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META TOPICPARENT name="WebHome"

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CCPi links and work carried out within SCD/STFC and related parties. This wiki is a community site to update on administrative (EPSRC / SCD) targets and discussion points.

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CCPi aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. There are parts; not least reconstruction techniques to create a 3D volume data set from projections and quantification techniques that can extract relevant objective values from these 3D volumes.
>
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The CCPi network was established in 2012 to support the emerging UK tomography community with a toolbox of algorithms to increase the quality and level of information that can be extracted by computed tomography. There are four major open source software parts supported: pre-processing techniques for image calibration and noise reduction; reconstruction techniques to create a 3D volume data set from projections; segmentation/quantification techniques that can extract relevant objective values from these 3D volumes; and a software framework development to enable the exploitation across a wide range of imaging devices.
  WP_20170612_013cw.jpg

The "Fringe" Meeting Monday 10 June 2019

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Invitation to the Fringe meeting: short informal presentations focusing on creating an Intelligent Framework: Pros and Cons of AI/ML in the Computed Tomography pipeline framework with support and sponsorship from The Alan Turing Institute
>
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Invitation to the Fringe meeting: short informal presentations focusing on creating an Intelligent Framework: Pros and Cons of AI/ML in the Computed Tomography pipeline with support and sponsorship from The Alan Turing Institute
  ATI_logo_black_W1024px.jpg

Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991

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The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.
>
>
The event will focus on essential, and past, AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.
 
Changed:
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MONDAY 10 June 2019:
>
>
MONDAY 10 June 2019: In main Piccavance Theatry (Harwell - RAL)
 
  • 10am-1030am Coffee and biscuits
  • 10:30am CCPi Working Group event in AVF (Harwell Campus, Atlas Building)
Changed:
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    • Register at: " target="_blank">https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u]]
  • 12noon Working Lunch with Working Group of CCPi
    • Specialist lunch-and-Learn talk by Joe Kelleher on EnginX
  • 1:30pm-5:00pm Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
  • With 2:30pm: Coffee and cookies etc.
    • Talks by key indivisuals
    • Demonstration of cross-platform analytical-vis and frameworks
>
>
    • Agenda:
      • Network Funds requested and short-term fellowships
      • LoS (Letters of Support) requests
      • Announcement - 5 year plan for 2020-2025
      • Hackathon #4
      • Update on CIL Core Imaging Library
      • Update on multispectral Flagship grant
    • Register (just for the Working Group) at: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u
  • 12noon-12:45pm Lunch-and-Learn Specialist Talk - ALL invited
    • Joe Kelleher on EnginX
  • 12:45pm-1:45pm Lunch
  • 1:45pm-4:30pm The Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
  • The Fringe Agenda
    • 1:45pm-2:00pm Summary of needs document; and intro to CCPi requiremnets and STFC facilities available (MT and EP@CCPi)
    • 2:00pm-2:20pm Ada Lovelace Centre and ATI Fellowship demo (JT@STFC, WK@UoWarwick)
    • 2:20pm-3:00pm Talks by (AH@CWI) and key individuals 3x10mins (DR@MINES, MB@DLS, XY@DESY)
    • 3:00pm-3:30pm Coffee and Muffins
    • 3:30pm-4:30pm Talks continue (BC@UoBirmingham, JM@UCL) and exercise round-table pointers
 
  • Finish at 5pm
Changed:
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Plan on links to dinner reception with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.
>
>
Plan on links to speakers event with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.
 

Past Topics:

Line: 40 to 51
 
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:
Changed:
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  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
>
>
  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests'
 
  1. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  2. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
Changed:
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
>
>
  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
 
  1. * Jingyi Mo University College London ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’
  2. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre AI-Vision
Changed:
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  1. * W. Kendall, Warwick University
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  1. * Wilfrid Kendall, Warwick University
  2. * Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
 
  1. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  2. Dan Bull, University of Southampton ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’
Deleted:
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  1. * probable: Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
 
  1. * possible; Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
  2. ...
  3. with 3DM sponsorship.

Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk

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Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
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Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
 
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Video Conf link - Physically based at the Atlas Visualation Facility (Atlas Buildng, Harwell Campus)
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Video Conf link - Physically based RAL - Harwell Campus
  • Join Zoom Meeting: https://ukri.zoom.us/j/352946090
 
  • One tap mobile +442036950088,,352946090# United Kingdom +442039663809,,352946090# United Kingdom
Changed:
<
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  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
>
>
  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
  TUESDAY 11 June 2019
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
  WEDNESDAY 12 and THURSDAY 13 June 2019
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 CCP hackathn #4 - 12-13 June 2019 after the Workshops in RAL; a topic will be inviting the Diamond Light Source developers to see how to mix the CCPi software and Flagship python framework system, more effectively with savu.

Last year's event, 2018

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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
 
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
  pano57w.jpg
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  WP_20180614_002plus_w.jpg
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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 p20180614_193711_13p40w.jpg

<a name="WorkingGroup"></a>

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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
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  Register here:
Changed:
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https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
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https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
  Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
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    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
  2. A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
Changed:
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
>
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
 
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
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  • to hand-hold transfer-code development for "the Astra Toolbox for CT reconstructions of data from the Nikon 225" for Llion Evans
  • for hackathon in April 2019 (see below)
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  • for https://www.turing.ac.uk/events/data-centric-materials-science-and-engineering involving advertisement and attendance
  • for http://dxct.hud.ac.uk/ in June 2019 - proposed support for student attendance; and CCPi stand to be made available
  • for https://mecheng.ucl.ac.uk/imagingbiopro/ only advertisement
 
  • LoS New Investigator Award EPSRC proposal 'Limited Data X-ray CT for Measurement'
Changed:
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  • for Fringe event in June 2019 prior to Advances in Xray Imaging http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiTomo
 
  • ...
  • Other Links: ToScA UK need contacting
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  3. CIL Build-and-Test automation (from Tomas Kulhanek)
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  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
 
  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`

4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm

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  • Atlas Visualisation Facility at Harwell Campus (RAL) and
  • ... ICAM building at University of Manchester and
Changed:
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  • ... by video-conference through https://ukri-stfc.zoom.us/j/418481169
  For catering please email if you wish to attend: martin.turner@manchester.ac.uk
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  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on code C01
  • SCARF18 - should be open for SCD staff
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  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
  Accepted (11): Mark Basham, Mark Williams, M Soleimani, Martin Turner, Martyn Winn, Parmesh Gajar, Jay Warnett, Phil Withers, Edo Pasca, Evangelos (Vaggelis) Papoutsellis, Bob Cernik, Bill Lionheart
Line: 416 to 427
 
  • CCPi Fellowships approved and visits: Brian Bay x2 as well as summer visitors (mainly at dXCT).
  • Grants submitted with Letters of Support from CCPi: WMG is approved.
  • Joint CCP hackathon - workshops/events on code integration
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  • Lunch-and-Learn and Show-and-Tell events: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars
  CCPi conferences and workshops: Summer 2018
Line: 426 to 437
 
  • ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
  2. CIL-Core development: linking with Flagship software
Line: 438 to 449
 Papers etc:

  • TomoPhantom software and paper:https://github.com/dkazanc/TomoPhantom
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  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
 
  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop
Line: 452 to 463
 
  • Website and email list (review by EP/MT)
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
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  • Beamtime; 4 September 2018 Advanced Radiotherapy https://www.birmingham.ac.uk/research/activity/nuclear/about-us/Facilities.aspx with Swansea
 
  • Beamtime; IMAT February 2019

Points Raised with more details: from November 2017 meeting:

Line: 467 to 478
  Other items:
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  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
 
  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

Line: 501 to 512
 Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 
  1. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  2. Are you involved in any eCSE projects (please provide details)? No
  3. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
Line: 533 to 544
  Other points:
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  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
 
  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)
Line: 589 to 600
 
  1. Elizabeth.Surrey@
  2. rob.akers@
  3. daniel.pooley@
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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

 
Changed:
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
Line: 632 to 643
 
    • distibution jiscmail lists
    • website content etc
    • HPC: SCARF18, Archer access.
Changed:
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  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
 
  • AOB
    • Location for next WG at RAL
    • GDPR issues
Line: 660 to 671
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

 
Exec Meeting Agenda (Nov 2017 - Mar 2018) 29 March 2018, 9:30am "To discuss the new coding and outcomes from the Core and Flagship environment"
Line: 682 to 693
 
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
Changed:
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
  - dimension XCT: speakers so far (plus one) July 2018 ACTION Requested funds for travel for students on usual basis
Line: 736 to 747
 
  • Software to generate 2D-4D analytical phantoms and their Radon transforms for image processing
  • Paper submitted to Software X
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  • Code available at https://github.com/dkazanc/TomoPhantom
 
Changed:
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  Extra:
Line: 750 to 761
 
  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
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    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
 
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
Line: 766 to 777
 
  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
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  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
  Training / Seminar:

  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
Changed:
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  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
 
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
Changed:
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  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
 
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
Line: 817 to 828
 
  • 6 December 2017 - Flagship-IMAT meeting in RAL to update on progress.
  • Flagship-CIL code-sprint 5-8 March 2018 - plan to repeat.
Changed:
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  • 12 December 2017 EPSRC XCT Tomography Equipment Roadmap, Townhall Meeting (Manchester) https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
 
  • 29 January - 9 February 2018 ISO / TC 213 WG10 standards meeting at BSI (389 Chiswick High Road, London E4 4AL). In the first week, Monday and Tuesday 9am-12noon XCT general topics; and Wednesday 3pm-5:30pm & Friday 9am-11:30am ISO Cttee deliberations.

Appendix A: details of events November 2017 - May 2018

Line: 842 to 853
  Agenda 10:30am coffee - meeting 11am-2pm including Lunch
Changed:
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
  Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
Line: 882 to 893
 
  • (10 mins) actions + further discussion
  • AOB
Changed:
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
 
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
Line: 891 to 902
 
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
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  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
 
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
Changed:
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  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
 
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
Line: 933 to 944
 
  • MT to write a summary for SCD newsletter on CCPi activities
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day
Changed:
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
 

CCPi Flagship session: 2pm-3:30pm

Items:

  • ISIS IMAT Phantom data acquisition process
Changed:
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  • Flagship items from grant and last June meeting: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiFlagship
 
  • Future meetings and integration
Changed:
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  • Additions to website: https://www.ccpi.ac.uk/Flagship
 
  • ...

Appendix A: details of events June 2016 - October 2017

Line: 1011 to 1022
  Atlas Visualisation Facility: Monday 12 June 2017 - registration at:
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  • Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-preadvances-in-x-ray-imaging-tickets-32623491742
 
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There will be video conferencing available: https://bluejeans.com/576183356/
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There will be video conferencing available: https://bluejeans.com/576183356/
  Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm

  • Approval of past six months activities (SN)
Changed:
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    • approval of secretariat roles (http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole)
 
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
Line: 1041 to 1052
 
    • Image / vidoe archive on website inc Flagship pics
    • ...
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
  Combined Presentation: CCPiJune2017WG_c.pdf
Line: 1070 to 1081
 Links: current EPSRC equipment Roadmap:
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
 

Networking and Funding Activities: December 2016 - May 2017

Line: 1078 to 1089
 
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
Changed:
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
 
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
  • Three exhibitions:
    • 4-18 November 2016 Supercomputing Videos and interactive volume visualisation system at Hartree Centre stand #1137:
Line: 1090 to 1101
 
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
    • Workshop on SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
Changed:
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    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
 
  • BSI Standards involvement:
    • 11 January 2017 BSI standards meeting of the XCT panel (TDW/4/4/1)
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    • XCT user meeting events@npl.co.uk 8 March 2017 https://www.eventbrite.co.uk/e/xct-user-meeting-registration-31024486073
 
  • Developers' days:
    • 20 March 2017 pre-Flagship meeting at RAL and 11 May 2017 telephone-conf update.
  • Papers etc:
Line: 1102 to 1113
  Continual CCPi support for the three annual events:
Changed:
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
 
  1. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific Advancement symposium addressing hard and soft tissue imaging, understanding materials in 3D, recent advances in hardware and software, and a broad range of applications in tomography www.rms.org.uk/tosca2017

Coding Milestones : December 2016 - May 2017

Line: 1176 to 1187
 
  • Proposed Summer school in Tomo at Bath 2017
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)
  • Support for "short course /workshop as part of EGU2017. The subject would be automation of image analysis from large datasets using freeware. Probably I would focus on using imageJ."Jose Godinho
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  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf
 
CCPi Executive Summary, last six months: June 2016-November 2016

Line: 1194 to 1205
  Website refreshed and data archives in use (zenodo and dropbox for business are now available).
Changed:
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https://www.ccpi.ac.uk/
 
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https://zenodo.org/communities/ccpi/?page=1&size=20
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https://zenodo.org/communities/ccpi/?page=1&size=20
 

Coding Milestones from the core SLA funds: To be discussed.

Current set for 2016-2017 are:

Line: 1213 to 1224
 
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
Changed:
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
  Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.
Line: 1234 to 1245
 
  • ... link to S-J C and MT for sections
  • CECAM event at DL – on Drishti / Avizo
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
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  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
 
  • EU COST grant: application for 2017

Proposals (speculative):

Line: 1264 to 1275
 
  • Logos on stickers and mugs
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.
Changed:
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 

Appendix B – details of events June 2016-November 2016

Line: 1287 to 1298
 
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU:https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
Changed:
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  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
 
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Line: 1298 to 1309
 
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
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  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
  Training ; six advertised:
Line: 1455 to 1466
  - Infrastructure:
Changed:
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
  Update with touchscreen items (link to ICAL Russell Garwood).
Line: 1508 to 1519
 
  1. memory management to be improved esp for 3D data
  2. rotation based optimisation
Changed:
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
  slicerRT is more possibly more about the "quantification" of the processed data while the stir project is more about the reconstruction methods.
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  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
 
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.
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  Deliverables produced:
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
  “4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
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Reconstruction Toolkit:

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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
  Core Workplan: 0.5 FTE

Items from discussion:

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  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
Line: 1809 to 1820
  Co-ordinate collaboration with CCPASEArch; ASEArch activites include work with Evgueni Ovtchinnikov commencing 1 April 2014: This work is ASEArch related and is specific to that cost code. The work involves numberical methods, to apply a multigrid solution to improve the issues caused by a gradient based regulisation coefficient, as applied to an iterative CGM (Conjugate Gradient Method) that is coordinated by the CCPi Flagship fellow, Daniil Kazantsev. These activities are in their very early stages to improve the convergence of the algorithm but requires data analysis.
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
 
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
 

Quantification Toolkit:

The quantification toolkit involved integration of code within Avizo, VolView and possibly ImageJ (and possibly Drishti); (Note now ParaView does volume visualisation this is an option as well).

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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
  Core Workplan: 0.5 FTE

Items from discussion:

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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
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  Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
 
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
  Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
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  Papers etc.:
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
  Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.
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  CCPi monitors/promotes various training courses including
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  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
 
  • 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data. (Day 1: Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) (Day 2: Introduction to Avizo Fire workshop (quantification), Analysis of inter-connected structures using Avizo and ImageJ)
  • Thursday 8 May 2014 - Aviso training - specialist session
  • June - week long session at University of Manchester
Line: 1894 to 1905
  Deliverables - Reconstruction and Quantification through the CCPi community
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Main website is at: http://www.ccpi.ac.uk/
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Main website is at: http://www.ccpi.ac.uk/
 

End of Project Targets

Revision 20023 May 2019 - MartinTurner

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 The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.

MONDAY 10 June 2019:

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  • CCPi Working Group pre-event and talks from 10am in AVF (Harwell Campus, Atlas Building)
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  • 10am-1030am Coffee and biscuits
  • 10:30am CCPi Working Group event in AVF (Harwell Campus, Atlas Building)
 
    • Register at: " target="_blank">https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u]]
  • 12noon Working Lunch with Working Group of CCPi
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    • Specialist lunch-and-Learn taslk by Joe Kelleher on EnginX
  • From 1:30pm Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
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    • Specialist lunch-and-Learn talk by Joe Kelleher on EnginX
  • 1:30pm-5:00pm Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
 
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  • From 1:30pm: Coffee and cookies etc.
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  • With 2:30pm: Coffee and cookies etc.
    • Talks by key indivisuals
 
  • Demonstration of cross-platform analytical-vis and frameworks
  • Finish at 5pm

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  • 12noon Working Lunch with Working Group of CCPi
    • Specialist lunch-and-Learn taslk by Joe Kelleher on EnginX
  • From 1:30pm Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
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  • From 1:30pm: Coffee and cookies etc.
  • Demonstration of cross-platform analytical-vis and frameworks
  • Finish at 5pm

Revision 19814 May 2019 - MartinTurner

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  ATI_logo_black_W1024px.jpg
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Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
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Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
  The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.
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Past Topics:

2019 Fringe Pros and Cons of AI/ML in the CT pipeline
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2018 Fringe Cross reconstruction Software Sharing tehniques
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2018 Fringe Cross reconstruction Software Sharing techniques
 
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
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Speakers at Advance Workshop and Fringe (*) are from a range of international institutions, include:
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Speakers at Advance Workshop and The Fringe (*) are from a range of international institutions, include:

 
  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
 
  1. * Jingyi Mo University College London ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’
  2. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre AI-Vision
  3. * W. Kendall, Warwick University
  4. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
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  1. Dan Bull, University of Southampton ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’
  2. * probable: Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
  3. * possible; Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
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  1. Dan Bull, University of Southampton ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’
  2. * probable: Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
  3. * possible; Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
 
  1. ...
  2. with 3DM sponsorship.
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  Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
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Video Conf link - Physically based at the Atlas Visualation Facility (Atlas Buildng, Harwell Campus)
  • Join Zoom Meeting: https://ukri.zoom.us/j/352946090
  • One tap mobile +442036950088,,352946090# United Kingdom +442039663809,,352946090# United Kingdom
  • Dial by your location +44 203 695 0088 United Kingdom +44 203 966 3809 United Kingdom 800 031 5717 United Kingdom Toll-free Meeting ID: 352 946 090 Find your local number: https://zoom.us/u/aciV4M2Fbn
 TUESDAY 11 June 2019
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
  WEDNESDAY 12 and THURSDAY 13 June 2019
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 CCP hackathn #4 - 12-13 June 2019 after the Workshops in RAL; a topic will be inviting the Diamond Light Source developers to see how to mix the CCPi software and Flagship python framework system, more effectively with savu.

Last year's event, 2018

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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
 
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
  pano57w.jpg
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  WP_20180614_002plus_w.jpg
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
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  Register here:
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https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
  Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
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    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
  2. A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
 
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
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  • to hand-hold transfer-code development for "the Astra Toolbox for CT reconstructions of data from the Nikon 225" for Llion Evans
  • for hackathon in April 2019 (see below)
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  • for https://www.turing.ac.uk/events/data-centric-materials-science-and-engineering involving advertisement and attendance
  • for http://dxct.hud.ac.uk/ in June 2019 - proposed support for student attendance; and CCPi stand to be made available
  • for https://mecheng.ucl.ac.uk/imagingbiopro/ only advertisement
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  • LoS New Investigator Award EPSRC proposal 'Limited Data X-ray CT for Measurement'
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  • for Fringe event in June 2019 prior to Advances in Xray Imaging http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiTomo
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  • ...
  • Other Links: ToScA UK need contacting
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  3. CIL Build-and-Test automation (from Tomas Kulhanek)
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  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
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  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`

4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm

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  • Atlas Visualisation Facility at Harwell Campus (RAL) and
  • ... ICAM building at University of Manchester and
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  • ... by video-conference through https://ukri-stfc.zoom.us/j/418481169
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  For catering please email if you wish to attend: martin.turner@manchester.ac.uk
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  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on code C01
  • SCARF18 - should be open for SCD staff
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  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
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  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
  Accepted (11): Mark Basham, Mark Williams, M Soleimani, Martin Turner, Martyn Winn, Parmesh Gajar, Jay Warnett, Phil Withers, Edo Pasca, Evangelos (Vaggelis) Papoutsellis, Bob Cernik, Bill Lionheart
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  • CCPi Fellowships approved and visits: Brian Bay x2 as well as summer visitors (mainly at dXCT).
  • Grants submitted with Letters of Support from CCPi: WMG is approved.
  • Joint CCP hackathon - workshops/events on code integration
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  • Lunch-and-Learn and Show-and-Tell events: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars
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  CCPi conferences and workshops: Summer 2018
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  • ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
  2. CIL-Core development: linking with Flagship software
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 Papers etc:

  • TomoPhantom software and paper:https://github.com/dkazanc/TomoPhantom
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  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
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  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop
Line: 444 to 451
 
  • Website and email list (review by EP/MT)
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
Changed:
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  • Beamtime; 4 September 2018 Advanced Radiotherapy https://www.birmingham.ac.uk/research/activity/nuclear/about-us/Facilities.aspx with Swansea
>
>
 
  • Beamtime; IMAT February 2019

Points Raised with more details: from November 2017 meeting:

Line: 459 to 466
  Other items:
Changed:
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  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
>
>
 
  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

Line: 493 to 500
 Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
Changed:
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<
  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
>
>
  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 
  1. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  2. Are you involved in any eCSE projects (please provide details)? No
  3. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
Line: 525 to 532
  Other points:
Changed:
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  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
>
>
 
  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)
Line: 581 to 588
 
  1. Elizabeth.Surrey@
  2. rob.akers@
  3. daniel.pooley@
Changed:
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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

>
>

CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

 
Changed:
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
>
>
Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
Line: 624 to 631
 
    • distibution jiscmail lists
    • website content etc
    • HPC: SCARF18, Archer access.
Changed:
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  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
>
>
 
  • AOB
    • Location for next WG at RAL
    • GDPR issues
Line: 652 to 659
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
Changed:
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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

>
>

CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

 
Exec Meeting Agenda (Nov 2017 - Mar 2018) 29 March 2018, 9:30am "To discuss the new coding and outcomes from the Core and Flagship environment"
Line: 674 to 681
 
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
Changed:
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
>
>
- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
  - dimension XCT: speakers so far (plus one) July 2018 ACTION Requested funds for travel for students on usual basis
Line: 728 to 735
 
  • Software to generate 2D-4D analytical phantoms and their Radon transforms for image processing
  • Paper submitted to Software X
Changed:
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  • Code available at https://github.com/dkazanc/TomoPhantom
>
>
 
Changed:
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
>
>
Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  Extra:
Line: 742 to 749
 
  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
Changed:
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    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
>
>
 
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
Line: 758 to 765
 
  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
Changed:
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  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
>
>
  Training / Seminar:

  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
Changed:
<
<
  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
>
>
 
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
Changed:
<
<
  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
>
>
 
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
Line: 809 to 816
 
  • 6 December 2017 - Flagship-IMAT meeting in RAL to update on progress.
  • Flagship-CIL code-sprint 5-8 March 2018 - plan to repeat.
Changed:
<
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  • 12 December 2017 EPSRC XCT Tomography Equipment Roadmap, Townhall Meeting (Manchester) https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
>
>
 
  • 29 January - 9 February 2018 ISO / TC 213 WG10 standards meeting at BSI (389 Chiswick High Road, London E4 4AL). In the first week, Monday and Tuesday 9am-12noon XCT general topics; and Wednesday 3pm-5:30pm & Friday 9am-11:30am ISO Cttee deliberations.

Appendix A: details of events November 2017 - May 2018

Line: 834 to 841
  Agenda 10:30am coffee - meeting 11am-2pm including Lunch
Changed:
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<
Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
>
>
Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
  Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
Line: 874 to 881
 
  • (10 mins) actions + further discussion
  • AOB
Changed:
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<
ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
>
>
ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
 
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
Line: 883 to 890
 
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
Changed:
<
<
  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
>
>
 
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
Changed:
<
<
  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
>
>
 
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
Line: 925 to 932
 
  • MT to write a summary for SCD newsletter on CCPi activities
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day
Changed:
<
<
General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
>
>
General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
 

CCPi Flagship session: 2pm-3:30pm

Items:

  • ISIS IMAT Phantom data acquisition process
Changed:
<
<
  • Flagship items from grant and last June meeting: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiFlagship
>
>
 
  • Future meetings and integration
Changed:
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<
  • Additions to website: https://www.ccpi.ac.uk/Flagship
>
>
 
  • ...

Appendix A: details of events June 2016 - October 2017

Line: 1003 to 1010
  Atlas Visualisation Facility: Monday 12 June 2017 - registration at:
Changed:
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  • Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-preadvances-in-x-ray-imaging-tickets-32623491742
>
>
 
Changed:
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There will be video conferencing available: https://bluejeans.com/576183356/
>
>
There will be video conferencing available: https://bluejeans.com/576183356/
  Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm

  • Approval of past six months activities (SN)
Changed:
<
<
    • approval of secretariat roles (http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole)
>
>
 
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
Line: 1033 to 1040
 
    • Image / vidoe archive on website inc Flagship pics
    • ...
Changed:
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
>
>
Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
  Combined Presentation: CCPiJune2017WG_c.pdf
Line: 1062 to 1069
 Links: current EPSRC equipment Roadmap:
Changed:
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
>
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
 

Networking and Funding Activities: December 2016 - May 2017

Line: 1070 to 1077
 
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
Changed:
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
>
>
    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
 
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
  • Three exhibitions:
    • 4-18 November 2016 Supercomputing Videos and interactive volume visualisation system at Hartree Centre stand #1137:
Line: 1082 to 1089
 
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
    • Workshop on SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
Changed:
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    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
>
>
 
  • BSI Standards involvement:
    • 11 January 2017 BSI standards meeting of the XCT panel (TDW/4/4/1)
Changed:
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    • XCT user meeting events@npl.co.uk 8 March 2017 https://www.eventbrite.co.uk/e/xct-user-meeting-registration-31024486073
>
>
 
  • Developers' days:
    • 20 March 2017 pre-Flagship meeting at RAL and 11 May 2017 telephone-conf update.
  • Papers etc:
Line: 1094 to 1101
  Continual CCPi support for the three annual events:
Changed:
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
>
>
  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
 
  1. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific Advancement symposium addressing hard and soft tissue imaging, understanding materials in 3D, recent advances in hardware and software, and a broad range of applications in tomography www.rms.org.uk/tosca2017

Coding Milestones : December 2016 - May 2017

Line: 1168 to 1175
 
  • Proposed Summer school in Tomo at Bath 2017
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)
  • Support for "short course /workshop as part of EGU2017. The subject would be automation of image analysis from large datasets using freeware. Probably I would focus on using imageJ."Jose Godinho
Changed:
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  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf
>
>
 
CCPi Executive Summary, last six months: June 2016-November 2016

Line: 1186 to 1193
  Website refreshed and data archives in use (zenodo and dropbox for business are now available).
Changed:
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<
https://www.ccpi.ac.uk/
>
>
https://www.ccpi.ac.uk/
 
Changed:
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https://zenodo.org/communities/ccpi/?page=1&size=20
>
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https://zenodo.org/communities/ccpi/?page=1&size=20
 

Coding Milestones from the core SLA funds: To be discussed.

Current set for 2016-2017 are:

Line: 1205 to 1212
 
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
Changed:
<
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
>
>
We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
  Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.
Line: 1226 to 1233
 
  • ... link to S-J C and MT for sections
  • CECAM event at DL – on Drishti / Avizo
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
Changed:
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  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
>
>
 
  • EU COST grant: application for 2017

Proposals (speculative):

Line: 1256 to 1263
 
  • Logos on stickers and mugs
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.
Changed:
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
>
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 

Appendix B – details of events June 2016-November 2016

Line: 1279 to 1286
 
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU:https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
Changed:
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  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
>
>
 
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Line: 1290 to 1297
 
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
Changed:
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  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
>
>
  Training ; six advertised:
Line: 1447 to 1454
  - Infrastructure:
Changed:
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
>
>
1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
  Update with touchscreen items (link to ICAL Russell Garwood).
Line: 1500 to 1507
 
  1. memory management to be improved esp for 3D data
  2. rotation based optimisation
Changed:
<
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
>
>
Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
  slicerRT is more possibly more about the "quantification" of the processed data while the stir project is more about the reconstruction methods.
Line: 1553 to 1560
 
  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
Changed:
<
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
>
>
 
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.
Line: 1739 to 1746
  Deliverables produced:
Changed:
<
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
>
>
Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
  “4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
Line: 1781 to 1788
 

Reconstruction Toolkit:

Changed:
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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
>
>
The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
  Core Workplan: 0.5 FTE

Items from discussion:

Changed:
<
<

>
>

 
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
Line: 1801 to 1808
  Co-ordinate collaboration with CCPASEArch; ASEArch activites include work with Evgueni Ovtchinnikov commencing 1 April 2014: This work is ASEArch related and is specific to that cost code. The work involves numberical methods, to apply a multigrid solution to improve the issues caused by a gradient based regulisation coefficient, as applied to an iterative CGM (Conjugate Gradient Method) that is coordinated by the CCPi Flagship fellow, Daniil Kazantsev. These activities are in their very early stages to improve the convergence of the algorithm but requires data analysis.
Changed:
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
 
Changed:
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
>
>
- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
 

Quantification Toolkit:

The quantification toolkit involved integration of code within Avizo, VolView and possibly ImageJ (and possibly Drishti); (Note now ParaView does volume visualisation this is an option as well).

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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
  Core Workplan: 0.5 FTE

Items from discussion:

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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
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  Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
>
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
 
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
>
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
  Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
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  Papers etc.:
Changed:
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
>
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
  Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.
Line: 1874 to 1881
  CCPi monitors/promotes various training courses including
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  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
>
>
 
  • 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data. (Day 1: Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) (Day 2: Introduction to Avizo Fire workshop (quantification), Analysis of inter-connected structures using Avizo and ImageJ)
  • Thursday 8 May 2014 - Aviso training - specialist session
  • June - week long session at University of Manchester
Line: 1886 to 1893
  Deliverables - Reconstruction and Quantification through the CCPi community
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Main website is at: http://www.ccpi.ac.uk/
 

End of Project Targets

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Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
  The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.

Revision 19613 May 2019 - MartinTurner

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  • CCPi Working Group pre-event and talks from 10am in AVF (Harwell Campus, Atlas Building)
    • Register at: " target="_blank">https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u]]
  • 12noon Working Lunch with Working Group of CCPi
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    • Specialist lunch-and-Learn taslk by Joe Kelleher on EnginX
>
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    • Specialist lunch-and-Learn taslk by Joe Kelleher on ! EnginX
 
  • From 1:30pm Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
  • From 1:30pm: Coffee and cookies etc.
  • Demonstration of cross-platform analytical-vis and frameworks
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  1. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre AI-Vision
  2. * W. Kendall, Warwick University
  3. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
Deleted:
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  1. Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
 
  1. Dan Bull, University of Southampton ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’
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  1. * Probable: Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
>
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  1. * probable: Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
  2. * possible; Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
 
  1. ...
  2. with 3DM sponsorship.

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  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
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  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
>
>
  1. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
 
  1. * Jingyi Mo University College London ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’
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  1. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  2. * W. Kendall, Warwick University:
>
>
  1. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre AI-Vision
  2. * W. Kendall, Warwick University
 
  1. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  2. Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
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  1. ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’, Dan Bull, University of Southampton
  2. Probable: Allard Hendriksen from CWI
>
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  1. Dan Bull, University of Southampton ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’
  2. * Probable: Allard Hendriksen from CWI..."currently working on ways of adapting data acquisition specifically for machine learning purposes, for example to avoid the need to acquire large amounts of training data"
 
  1. ...
  2. with 3DM sponsorship.

Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk

Added:
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Registration: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
 TUESDAY 11 June 2019

4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619

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>
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Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
  The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.

MONDAY 10 June 2019:

Changed:
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  • CCPi Working Group pre-event and talks from 10am
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  • CCPi Working Group pre-event and talks from 10am in AVF (Harwell Campus, Atlas Building)
    • Register at: " target="_blank">https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9URVFUVEFNSU43WEdMRlpMVlg4OUZSUjlSMC4u]]
 
  • 12noon Working Lunch with Working Group of CCPi
Added:
>
>
    • Specialist lunch-and-Learn taslk by Joe Kelleher on EnginX
  • From 1:30pm Fringe meeting - Pros and Cons of AI/ML in the CT pipeline
 
  • From 1:30pm: Coffee and cookies etc.
  • Demonstration of cross-platform analytical-vis and frameworks
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  • From 2:30pm: Discussion and short talks
>
>
  • Finish at 5pm
  Plan on links to dinner reception with RAL Advances in X-ray Imaging Workshop (11 June 2019) whose aim is to bring scientists from different fields to discuss developments and applications of a variety of X-ray imaging and complementary techniques, and to build international collaborations.
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2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Speakers at Advance Workshop and Fringe (*) are from a range of international institutions, include:
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  1. () *David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. () *Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
  4. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  5. () *Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  6. ‘Virtual CT with complex scanning trajectories in aRTist’, Carsten Bellon, BAM Federal Institute for Materials Research and Testing
  7. Probable: Allard Hendriksen from CWI
  8. ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’, Jingyi Mo, University College London
  9. (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  10. ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’, Dan Bull, University of Southampton
  11. Warwick University: W. Kendall
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  1. * David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. * Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. * Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
  4. * Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  5. * Jingyi Mo University College London ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’
  6. * Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  7. * W. Kendall, Warwick University:
  8. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  9. Carsten Bellon, BAM Federal Institute for Materials Research and Testing ‘Virtual CT with complex scanning trajectories in aRTist’
  10. ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’, Dan Bull, University of Southampton
  11. Probable: Allard Hendriksen from CWI
 
  1. ...
  2. with 3DM sponsorship.
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  TUESDAY 11 June 2019
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
>
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4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
  WEDNESDAY 12 and THURSDAY 13 June 2019
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 Open invitation but email: martin.turner@manchester.ac.uk or edoardo.pasca@stfc.ac.uk

CCP hackathn #4 - 12-13 June 2019 after the Workshops in RAL; a topic will be inviting the Diamond Light Source developers to see how to mix the CCPi software and Flagship python framework system, more effectively with savu.

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Last year's event, 2018,

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Last year's event, 2018

 
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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
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Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695
 
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
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On 15 June 2018, RAL Advances in X-ray Imaging Workshop; Register and deatails at: https://3rd-advances-in-xray-imaging-workshop.eventbrite.co.uk
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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Linked in positive feedback: https://www.linkedin.com/feed/update/activity:6413430689177362432/
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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
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  Register here:
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https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
  Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
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    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
  2. A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
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    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
 
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
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  • to hand-hold transfer-code development for "the Astra Toolbox for CT reconstructions of data from the Nikon 225" for Llion Evans
  • for hackathon in April 2019 (see below)
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  • for https://www.turing.ac.uk/events/data-centric-materials-science-and-engineering involving advertisement and attendance
  • for http://dxct.hud.ac.uk/ in June 2019 - proposed support for student attendance; and CCPi stand to be made available
  • for https://mecheng.ucl.ac.uk/imagingbiopro/ only advertisement
 
  • LoS New Investigator Award EPSRC proposal 'Limited Data X-ray CT for Measurement'
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  • for Fringe event in June 2019 prior to Advances in Xray Imaging http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiTomo
 
  • ...
  • Other Links: ToScA UK need contacting
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  3. CIL Build-and-Test automation (from Tomas Kulhanek)
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  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
 
  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`

4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm

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  • Atlas Visualisation Facility at Harwell Campus (RAL) and
  • ... ICAM building at University of Manchester and
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  • ... by video-conference through https://ukri-stfc.zoom.us/j/418481169
  For catering please email if you wish to attend: martin.turner@manchester.ac.uk
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  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on code C01
  • SCARF18 - should be open for SCD staff
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  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
>
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Grants: EU COST (Nov 2018), https://erc.europa.eu/funding/starting-grants and https://erc.europa.eu/funding/consolidator-grants (Feb 2019)
  Accepted (11): Mark Basham, Mark Williams, M Soleimani, Martin Turner, Martyn Winn, Parmesh Gajar, Jay Warnett, Phil Withers, Edo Pasca, Evangelos (Vaggelis) Papoutsellis, Bob Cernik, Bill Lionheart
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  • CCPi Fellowships approved and visits: Brian Bay x2 as well as summer visitors (mainly at dXCT).
  • Grants submitted with Letters of Support from CCPi: WMG is approved.
  • Joint CCP hackathon - workshops/events on code integration
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  • Lunch-and-Learn and Show-and-Tell events: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars
  CCPi conferences and workshops: Summer 2018
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  • ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
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  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
  2. CIL-Core development: linking with Flagship software
Line: 425 to 428
 Papers etc:

  • TomoPhantom software and paper:https://github.com/dkazanc/TomoPhantom
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  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
 
  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop
Line: 439 to 442
 
  • Website and email list (review by EP/MT)
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
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  • Beamtime; 4 September 2018 Advanced Radiotherapy https://www.birmingham.ac.uk/research/activity/nuclear/about-us/Facilities.aspx with Swansea
 
  • Beamtime; IMAT February 2019

Points Raised with more details: from November 2017 meeting:

Line: 454 to 457
  Other items:
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  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
 
  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

Line: 488 to 491
 Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
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  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 
  1. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  2. Are you involved in any eCSE projects (please provide details)? No
  3. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
Line: 520 to 523
  Other points:
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  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
 
  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)
Line: 576 to 579
 
  1. Elizabeth.Surrey@
  2. rob.akers@
  3. daniel.pooley@
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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

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CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

 
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
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Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship
  Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
Line: 619 to 622
 
    • distibution jiscmail lists
    • website content etc
    • HPC: SCARF18, Archer access.
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  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
 
  • AOB
    • Location for next WG at RAL
    • GDPR issues
Line: 647 to 650
  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

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CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

 
Exec Meeting Agenda (Nov 2017 - Mar 2018) 29 March 2018, 9:30am "To discuss the new coding and outcomes from the Core and Flagship environment"
Line: 669 to 672
 
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
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- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
  - dimension XCT: speakers so far (plus one) July 2018 ACTION Requested funds for travel for students on usual basis
Line: 723 to 726
 
  • Software to generate 2D-4D analytical phantoms and their Radon transforms for image processing
  • Paper submitted to Software X
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  • Code available at https://github.com/dkazanc/TomoPhantom
 
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
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Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  Extra:
Line: 737 to 740
 
  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
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    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
 
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
Line: 753 to 756
 
  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
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  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
  Training / Seminar:

  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
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  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
 
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
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  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
 
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
Line: 804 to 807
 
  • 6 December 2017 - Flagship-IMAT meeting in RAL to update on progress.
  • Flagship-CIL code-sprint 5-8 March 2018 - plan to repeat.
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  • 12 December 2017 EPSRC XCT Tomography Equipment Roadmap, Townhall Meeting (Manchester) https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
 
  • 29 January - 9 February 2018 ISO / TC 213 WG10 standards meeting at BSI (389 Chiswick High Road, London E4 4AL). In the first week, Monday and Tuesday 9am-12noon XCT general topics; and Wednesday 3pm-5:30pm & Friday 9am-11:30am ISO Cttee deliberations.

Appendix A: details of events November 2017 - May 2018

Line: 829 to 832
  Agenda 10:30am coffee - meeting 11am-2pm including Lunch
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
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Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
  Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
Line: 869 to 872
 
  • (10 mins) actions + further discussion
  • AOB
Changed:
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
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ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf
 
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
Line: 878 to 881
 
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
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  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
 
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
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  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
 
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
Line: 920 to 923
 
  • MT to write a summary for SCD newsletter on CCPi activities
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day
Changed:
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
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General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)
 

CCPi Flagship session: 2pm-3:30pm

Items:

  • ISIS IMAT Phantom data acquisition process
Changed:
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  • Flagship items from grant and last June meeting: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPiFlagship
 
  • Future meetings and integration
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  • Additions to website: https://www.ccpi.ac.uk/Flagship
 
  • ...

Appendix A: details of events June 2016 - October 2017

Line: 998 to 1001
  Atlas Visualisation Facility: Monday 12 June 2017 - registration at:
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  • Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-preadvances-in-x-ray-imaging-tickets-32623491742
 
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There will be video conferencing available: https://bluejeans.com/576183356/
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There will be video conferencing available: https://bluejeans.com/576183356/
  Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm

  • Approval of past six months activities (SN)
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    • approval of secretariat roles (http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole)
 
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
Line: 1028 to 1031
 
    • Image / vidoe archive on website inc Flagship pics
    • ...
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
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Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf
  Combined Presentation: CCPiJune2017WG_c.pdf
Line: 1057 to 1060
 Links: current EPSRC equipment Roadmap:
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
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https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/
 

Networking and Funding Activities: December 2016 - May 2017

Line: 1065 to 1068
 
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
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    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
 
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
  • Three exhibitions:
    • 4-18 November 2016 Supercomputing Videos and interactive volume visualisation system at Hartree Centre stand #1137:
Line: 1077 to 1080
 
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
    • Workshop on SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
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    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
 
  • BSI Standards involvement:
    • 11 January 2017 BSI standards meeting of the XCT panel (TDW/4/4/1)
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    • XCT user meeting events@npl.co.uk 8 March 2017 https://www.eventbrite.co.uk/e/xct-user-meeting-registration-31024486073
 
  • Developers' days:
    • 20 March 2017 pre-Flagship meeting at RAL and 11 May 2017 telephone-conf update.
  • Papers etc:
Line: 1089 to 1092
  Continual CCPi support for the three annual events:
Changed:
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
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  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
 
  1. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific Advancement symposium addressing hard and soft tissue imaging, understanding materials in 3D, recent advances in hardware and software, and a broad range of applications in tomography www.rms.org.uk/tosca2017

Coding Milestones : December 2016 - May 2017

Line: 1163 to 1166
 
  • Proposed Summer school in Tomo at Bath 2017
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)
  • Support for "short course /workshop as part of EGU2017. The subject would be automation of image analysis from large datasets using freeware. Probably I would focus on using imageJ."Jose Godinho
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  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf
 
CCPi Executive Summary, last six months: June 2016-November 2016

Line: 1181 to 1184
  Website refreshed and data archives in use (zenodo and dropbox for business are now available).
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https://www.ccpi.ac.uk/
 
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https://zenodo.org/communities/ccpi/?page=1&size=20
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https://zenodo.org/communities/ccpi/?page=1&size=20
 

Coding Milestones from the core SLA funds: To be discussed.

Current set for 2016-2017 are:

Line: 1200 to 1203
 
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
Changed:
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
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We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
  Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.
Line: 1221 to 1224
 
  • ... link to S-J C and MT for sections
  • CECAM event at DL – on Drishti / Avizo
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
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  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
 
  • EU COST grant: application for 2017

Proposals (speculative):

Line: 1251 to 1254
 
  • Logos on stickers and mugs
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.
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Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 

Appendix B – details of events June 2016-November 2016

Line: 1274 to 1277
 
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU:https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
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  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
 
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Line: 1285 to 1288
 
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
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  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
  Training ; six advertised:
Line: 1442 to 1445
  - Infrastructure:
Changed:
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
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1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en
  Update with touchscreen items (link to ICAL Russell Garwood).
Line: 1495 to 1498
 
  1. memory management to be improved esp for 3D data
  2. rotation based optimisation
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
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Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
  slicerRT is more possibly more about the "quantification" of the processed data while the stir project is more about the reconstruction methods.
Line: 1548 to 1551
 
  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
 
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.
Line: 1734 to 1737
  Deliverables produced:
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
>
>
Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
  “4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
Line: 1776 to 1779
 

Reconstruction Toolkit:

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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
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The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls
  Core Workplan: 0.5 FTE

Items from discussion:

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>
>

 
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
Line: 1796 to 1799
  Co-ordinate collaboration with CCPASEArch; ASEArch activites include work with Evgueni Ovtchinnikov commencing 1 April 2014: This work is ASEArch related and is specific to that cost code. The work involves numberical methods, to apply a multigrid solution to improve the issues caused by a gradient based regulisation coefficient, as applied to an iterative CGM (Conjugate Gradient Method) that is coordinated by the CCPi Flagship fellow, Daniil Kazantsev. These activities are in their very early stages to improve the convergence of the algorithm but requires data analysis.
Changed:
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
>
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EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)
 
Changed:
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- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
>
>
- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).
 

Quantification Toolkit:

The quantification toolkit involved integration of code within Avizo, VolView and possibly ImageJ (and possibly Drishti); (Note now ParaView does volume visualisation this is an option as well).

Changed:
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
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Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/
  Core Workplan: 0.5 FTE

Items from discussion:

Changed:
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>
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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
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  Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.
Changed:
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
>
>
A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
 
Changed:
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- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
>
>
- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
  Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
Line: 1849 to 1852
  Papers etc.:
Changed:
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
>
>
  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
  Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.
Line: 1869 to 1872
  CCPi monitors/promotes various training courses including
Changed:
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  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
 
  • 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data. (Day 1: Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) (Day 2: Introduction to Avizo Fire workshop (quantification), Analysis of inter-connected structures using Avizo and ImageJ)
  • Thursday 8 May 2014 - Aviso training - specialist session
  • June - week long session at University of Manchester
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  Deliverables - Reconstruction and Quantification through the CCPi community
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Main website is at: http://www.ccpi.ac.uk/
 

End of Project Targets

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  1. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  2. () *Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  3. ‘Virtual CT with complex scanning trajectories in aRTist’, Carsten Bellon, BAM Federal Institute for Materials Research and Testing
Changed:
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<
  1. Chris Simpson (Bristol Uni):
>
>
  1. Probable: Allard Hendriksen from CWI
 
  1. ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’, Jingyi Mo, University College London
  2. (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  3. ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’, Dan Bull, University of Southampton

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2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Speakers at Advance Workshop and Fringe (*) are from a range of international institutions, include:
Changed:
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  1. (*) David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. (*) Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
  4. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  5. (*) Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  6. Chris Simpson (Bristol Uni):
  7. (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  8. Warwick University: W. Kendall
>
>
  1. () *David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. () *Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
  4. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  5. () *Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  6. ‘Virtual CT with complex scanning trajectories in aRTist’, Carsten Bellon, BAM Federal Institute for Materials Research and Testing
  7. Chris Simpson (Bristol Uni):
  8. ‘Characterising the microstructural evolutional of solidification in ice cream using synchrotron X-ray tomography’, Jingyi Mo, University College London
  9. (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  10. ‘Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation’, Dan Bull, University of Southampton
  11. Warwick University: W. Kendall
 
  1. ...
  2. with 3DM sponsorship.

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2018 Fringe Cross reconstruction Software Sharing tehniques
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Changed:
<
<
Speakers at Advance Workshop and Fringe (*) are:

  • (*) David Ryckelynck (ParisTech, Paris): “Computer vision for reduced-order modeling of macroscopic mechanical tests”
  • Carsten Bellon (BAM Berlin): “Virtual CT with complex scanning trajectories in aRTist”
  • (*) Mark Basham (DLS):
  • Biao Cai (Birmingham Uni):
  • Azeem Mohammed (Leicester Uni):
  • Chris Simpson (Bristol Uni):
  • (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  • (*) Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  • ...
  • with 3DM sponsorship.
>
>
Speakers at Advance Workshop and Fringe (*) are from a range of international institutions, include:
  1. (*) David Ryckelynck, MINES Paristech 'Computer vision for reduced-order modelling of macroscopic mechanical tests' Carsten Bellon, BAM Federal Institute for Materials Research and Testing 'Virtual CT with complex scanning trajectories in aRTist'
  2. (*) Mark Basham, Diamond Light Source 'SuRVos: Speeding up Segmentation of Biological Imaging Volumes'
  3. Biao Cai, University of Birmingham '4D imaging and modelling applied to solidification and glass foaming.'
  4. Azeem Mohammed, University of Leicester 'Multiscale microstructural investigations in metallic materials using X-ray tomographic, WAXS and SAXS.
  5. (*) Xiaogang Yang DESY Photon Science https://xlearn.readthedocs.io/en/latest/
  6. Chris Simpson (Bristol Uni):
  7. (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  8. Warwick University: W. Kendall
  9. ...
  10. with 3DM sponsorship.
  Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk
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  p20180614_193711_13p40w.jpg
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CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.

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Working Group Meeting Agenda 10 June 2019, 11am

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Coffe and biscuits from 10am. Demo of something!!
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Coffe and biscuits from 10am. Demo of EnginX proposed.
 
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Hackathon results: 8-11 April 2019
>
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1. Actions from last meetings
 
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- go through list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- go through list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out.
>
>
1.1 Network funds spendt and proposed:
 
Changed:
<
<
- release of the BlockFramework with added documentation and examples
- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework
- Gemma and Parmesh are going to work at the Nikon scanner for some debug
- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this.
>
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2. Hackathon #3 & #4 review and planning: 8-11 April 2019 and 12-13 June 2019
 
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The regularisation toolkit's publication has been accepted and will be out soon and this is a good publicity for all our software.
>
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- list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out
- release of the ! BlockFramework with added documentation and example
- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework
- Gemma and Parmesh are going to work at the Nikon scanner for some debug
- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this.
 
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MSc projects:
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3. Publications: The regularisation toolkit's publication has been accepted.

4. MSc projects:

  - JJ "Martin Andersen at RAL on flat field modelling, I am co-supervising an MSc student from DTU with Martin building on that work. She will visit Manchester 13-16 May to try the methods on our IMAT data"

- BL/PW Michael White - 'consistency conditions for the neutron data' To work over the Summer

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New recruit at DLS: Shikhaliev, Polad (DLSLtd,RAL,SCI)
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5. New recruit at DLS: Shikhaliev, Polad (DLSLtd,RAL,SCI) and link to savu
 
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New data storage area path is \\nasr.man.ac.uk\epsrss$\snapped\replicated\CCPi_RTMCT
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6. New data storage area path is \\nasr.man.ac.uk\epsrss$\snapped\replicated\CCPi_RTMCT
 
Changed:
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... "CCPi. We had a version of your code on CCPi forge but I didn't do anything before they closed it. I am thinking we should dig it out again and with some help from Parmesh get some demo scripts for using with Nikon. Parmesh is also working on how to access the Zeiss system (I think) so we could do that too" to henry and gemma, BL
>
>
7. Haching Code results/updates ... "CCPi. We had a version of your code on CCPi forge but I didn't do anything before they closed it. I am thinking we should dig it out again and with some help from Parmesh get some demo scripts for using with Nikon. Parmesh is also working on how to access the Zeiss system (I think) so we could do that too" to henry and gemma, BL
 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Register here:

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 Core Imaging Library and Flagship coding Hackathon #4 - enable code ideas to be implement and released 'instantaneously' or after lots of coffee (and some testing).

Open invitation but email: martin.turner@manchester.ac.uk or edoardo.pasca@stfc.ac.uk

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CCP hackathn #4 - 12-13 June 2019 after the Workshops in RAL; a topic will be inviting the Diamond Light Source developers to see how to mix the CCPi software and Flagship python framework system, more effectively with savu.
 

Last year's event, 2018,

Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695

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 The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.

MONDAY 10 June 2019:

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  • CCPi Working Group pre-event and talks from 10am
 
  • 12noon Working Lunch with Working Group of CCPi
  • From 1:30pm: Coffee and cookies etc.
  • Demonstration of cross-platform analytical-vis and frameworks
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  • ...
  • with 3DM sponsorship.
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Fringe invites are out - if want to talk/argue send an email: martin.turner@manchester.ac.uk
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Fringe invites are now out - if want to talk/argue send an email: martin.turner@manchester.ac.uk
  TUESDAY 11 June 2019

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  The Flagships will focus events on essential, and past AI/ML experiences as well as work undertaken in the major imaging facilities including the Diamond Light Source and ISIS.
Added:
>
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MONDAY 10 June 2019:
 
  • 12noon Working Lunch with Working Group of CCPi
  • From 1:30pm: Coffee and cookies etc.
  • Demonstration of cross-platform analytical-vis and frameworks
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  • ...
  • with 3DM sponsorship.
Changed:
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Fringe invites are out - if wan't to talk/argue send an email: martin.turner@manchester.ac.u
>
>
Fringe invites are out - if want to talk/argue send an email: martin.turner@manchester.ac.uk
 
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4th Annual Workshop on Advances in X-ray Imaging at DLS 11 June 2019:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
>
>
TUESDAY 11 June 2019

4th Annual Workshop on Advances in X-ray Imaging at DLS:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619

WEDNESDAY 12 and THURSDAY 13 June 2019

Core Imaging Library and Flagship coding Hackathon #4 - enable code ideas to be implement and released 'instantaneously' or after lots of coffee (and some testing).

Open invitation but email: martin.turner@manchester.ac.uk or edoardo.pasca@stfc.ac.uk

 

Last year's event, 2018,

Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695

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  • Azeem Mohammed (Leicester Uni):
  • Chris Simpson (Bristol Uni):
  • (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
Added:
>
>
 
  • ...
  • with 3DM sponsorship.

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2018 Fringe Cross reconstruction Software Sharing tehniques
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Changed:
<
<
Speakers at Advance Workshop are:
>
>
Speakers at Advance Workshop and Fringe (*) are:
 
Changed:
<
<
  • David Ryckelynck (ParisTech, Paris): “Computer vision for reduced-order modeling of macroscopic mechanical tests”
>
>
  • (*) David Ryckelynck (ParisTech, Paris): “Computer vision for reduced-order modeling of macroscopic mechanical tests”
 
  • Carsten Bellon (BAM Berlin): “Virtual CT with complex scanning trajectories in aRTist”
Changed:
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<
  • Mark Basham (DLS):
>
>
  • (*) Mark Basham (DLS):
 
  • Biao Cai (Birmingham Uni):
  • Azeem Mohammed (Leicester Uni):
  • Chris Simpson (Bristol Uni):
Added:
>
>
  • (*) Jeyan Thiyagalingam - UKRI STFC <t.jeyan@stfc.ac.uk> ADA Lovelace Centre
  • ...
 
  • with 3DM sponsorship.
Changed:
<
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Fringe invites are going out - if wan't to talk/argue send an email: martin.turner@manchester.ac.uk
>
>
Fringe invites are out - if wan't to talk/argue send an email: martin.turner@manchester.ac.u
 
Added:
>
>
4th Annual Workshop on Advances in X-ray Imaging at DLS 11 June 2019:-
https://www.diamond.ac.uk/Home/Events/2019/Advances-in-X-ray-Imaging0.html
https://www.eventbrite.co.uk/e/the-4th-annual-advances-in-x-ray-imaging-workshop-tickets-59119701619
 

Last year's event, 2018,

Was on cross reconstruction Software Sharing tehniques: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695

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Added:
>
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... "CCPi. We had a version of your code on CCPi forge but I didn't do anything before they closed it. I am thinking we should dig it out again and with some help from Parmesh get some demo scripts for using with Nikon. Parmesh is also working on how to access the Zeiss system (I think) so we could do that too" to henry and gemma, BL
 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Register here:

Revision 18409 Apr 2019 - MartinTurner

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  New recruit at DLS: Shikhaliev, Polad (DLSLtd,RAL,SCI)
Added:
>
>
New data storage area path is \\nasr.man.ac.uk\epsrss$\snapped\replicated\CCPi_RTMCT
 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Register here:

Revision 18308 Apr 2019 - MartinTurner

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  Hackathon results: 8-11 April 2019
Changed:
<
<
- go through list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- go through list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out.

- release of the BlockFramework with added documentation and examples
- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework
- Gemma and Parmesh are going to work at the Nikon scanner for some debug
- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this.

>
>
- go through list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- go through list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out.

- release of the BlockFramework with added documentation and examples
- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework
- Gemma and Parmesh are going to work at the Nikon scanner for some debug
- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this.

  The regularisation toolkit's publication has been accepted and will be out soon and this is a good publicity for all our software.
Added:
>
>
MSc projects:

- JJ "Martin Andersen at RAL on flat field modelling, I am co-supervising an MSc student from DTU with Martin building on that work. She will visit Manchester 13-16 May to try the methods on our IMAT data"

- BL/PW Michael White - 'consistency conditions for the neutron data' To work over the Summer

New recruit at DLS: Shikhaliev, Polad (DLSLtd,RAL,SCI)

 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Revision 18205 Apr 2019 - MartinTurner

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META TOPICPARENT name="WebHome"

CCPi Tomographic Imaging

Line: 76 to 76
  Hackathon results: 8-11 April 2019
Changed:
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- go through list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- go through list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out.
>
>
- go through list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- go through list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out.

- release of the BlockFramework with added documentation and examples
- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework
- Gemma and Parmesh are going to work at the Nikon scanner for some debug
- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this.

 
Changed:
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- release of the BlockFramework with added documentation and examples
>
>
The regularisation toolkit's publication has been accepted and will be out soon and this is a good publicity for all our software.
 
Deleted:
<
<
- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework

- Gemma and Parmesh are going to work at the Nikon scanner for some debug

- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this. The regularisation toolkit's publication has been accepted and will be out soon and this is a good publicity for all our software

 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Revision 18105 Apr 2019 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

CCPi Tomographic Imaging

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  CCPi aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. There are parts; not least reconstruction techniques to create a 3D volume data set from projections and quantification techniques that can extract relevant objective values from these 3D volumes.
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WP_20170612_013cw.jpg
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WP_20170612_013cw.jpg
 

The "Fringe" Meeting Monday 10 June 2019

Invitation to the Fringe meeting: short informal presentations focusing on creating an Intelligent Framework: Pros and Cons of AI/ML in the Computed Tomography pipeline framework with support and sponsorship from The Alan Turing Institute

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ATI_logo_black_W1024px.jpg
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ATI_logo_black_W1024px.jpg
  Registation for the 2019 event at: https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-57975402991
Line: 31 to 31
 
2018 Fringe Cross reconstruction Software Sharing tehniques
2017 Fringe Building real needs within a National X-ray CT Roadmap
2016 Fringe Do we really need Synchrotrons
Deleted:
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 Speakers at Advance Workshop are:
Changed:
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  • David Ryckelynck (ParisTech, Paris): “Computer vision for reduced-order modeling of macroscopic mechanical tests”
  • Carsten Bellon (BAM Berlin): “Virtual CT with complex scanning trajectories in aRTist”
  • Mark Basham (DLS):
  • Biao Cai (Birmingham Uni):
  • Azeem Mohammed (Leicester Uni):
  • Chris Simpson (Bristol Uni):
  • with 3DM sponsorship.
>
>
  • David Ryckelynck (ParisTech, Paris): “Computer vision for reduced-order modeling of macroscopic mechanical tests”
  • Carsten Bellon (BAM Berlin): “Virtual CT with complex scanning trajectories in aRTist”
  • Mark Basham (DLS):
  • Biao Cai (Birmingham Uni):
  • Azeem Mohammed (Leicester Uni):
  • Chris Simpson (Bristol Uni):
  • with 3DM sponsorship.
  Fringe invites are going out - if wan't to talk/argue send an email: martin.turner@manchester.ac.uk
Line: 64 to 63
  p20180614_193711_13p40w.jpg
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<a name="exec" title="exec"></a>
 

CCPi Exec Meering (March 2019) and Working Group Meeting (10 June 2019 http://www.ccpi.ac.uk/)

Changed:
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Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
>
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Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
  Network targets: # of people / projects to gain impact items - What kind of code and bids: we should be preparing, in terms of best impacts
Added:
>
>

Working Group Meeting Agenda 10 June 2019, 11am

Coffe and biscuits from 10am. Demo of something!!

Hackathon results: 8-11 April 2019

- go through list of issues and clear all completed by the block framework and identify remaining outstanding ones to be in done for the release.
- go through list of pull requests and merge what is possible
- consider reorganising single-file modules processors.py, framework.py, reader.py as packages directories with separate py files.
- finish documentation of framework and optimisation
- move spdhg to a suitable place (either rewrite as Algorithm class or perhaps away from master branch and into a separate branch until it is ready)
- decide which demos from the wip folder should be available, rename wip as demos, and move other scripts elsewhere
- tidy up and improve documentation of CCPi-Astra and make FBP/FDK available. Also, if there are any inconsistencies between using ASTRA projectors and CCPi projectors, that should be ironed out.

- release of the BlockFramework with added documentation and examples

- have a look at Evelina's scripts and make a plan for further work and proper integration in the framework

- Gemma and Parmesh are going to work at the Nikon scanner for some debug

- We should also take some time to look at the calculation of the finite difference operator in multithreaded CPU/GPU that is already developed in the regularisation toolbox. I am very keen on pursuing this. The regularisation toolkit's publication has been accepted and will be out soon and this is a good publicity for all our software

 

Exec Meeting Agenda 12 March 2019, 12noon and 1pm

Changed:
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Register here:
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Register here:
  https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
Changed:
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Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
>
>
Location: Lovell Room, Alan Turing Building (3rd Floor) Manchester adn RAL (Harwel Campus) via videoconf:
 
Changed:
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Agenda:
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Agenda:
  0.1 12noon - Talks on Lunch-and Learn with Pizza

  1. Dan Symes and Ceri Brenner - HPL integration (and future synergistic): short update talk creating new sources
Changed:
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    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
>
>
    • "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.
  1. dimensional-XCT conference update from Huddersfield, Paul Bills
 
  1. A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
Changed:
<
<
    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
>
>
    • The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
  1. Introduction new staff and description of ICT'2019, Gemma Fardell
    • presenting her experiences to data including work at Nikon Metrolgy and some plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and I ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic."
  1. Network Activities
Line: 101 to 117
  Request for support
Changed:
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  • ...
Changed:
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  • Other Links: !ToScA UK need contacting
>
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  • Other Links: ToScA UK need contacting
  1.2 CCPi 16 (12) month review document including
Line: 118 to 134
  2. CIL-Core development: linking with Flagship software + papers etc
Changed:
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  • CIL/SIRF integration
  • CIL progresses (Vaggelis/Jakob present as link to Flagship)
  • DVC update
  • Next Hackathon - support package being provided on 9-12 April 2019
  • Flagship - Planning on attending AIP (Advanced Inverse Problems) in Grenoble.
>
>
  • CIL/SIRF integration
  • CIL progresses (Vaggelis/Jakob present as link to Flagship)
  • DVC update
  • Next Hackathon - support package being provided on 9-12 April 2019
  • Flagship - Planning on attending AIP (Advanced Inverse Problems) in Grenoble.
 
  • Core - attended iCT (February)

3. CIL Build-and-Test automation (from Tomas Kulhanek)

Changed:
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<
  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`
>
>
  • We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
  • General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
  • The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`
 
Changed:
<
<
4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm
>
>
4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm
  5. New updates to website: wishlist request
Line: 159 to 175
  Roll-over Future Ideas/Invitations:
Changed:
<
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  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
>
>
  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
 
  • Bath presentation (joint NPL project)
Changed:
<
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  • Future Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
>
>
  • Future Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
 
  • ...

Case Studies:

Changed:
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  • PE activities
  • beam hardening
  • quantification - porosity
  • parts of CIL
  • ULTRA integration
>
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  • PE activities
  • beam hardening
  • quantification - porosity
  • parts of CIL
  • ULTRA integration
  International Review:
Line: 208 to 224
  Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 406 subscribers; 7 new members since 5 October 2018
Changed:
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  1. evelina.ametova@
  2. gavin.taylor.01@
  3. evangelos.papoutsellis@
  4. oriol.roche.15@
  5. alan.clarke@
  6. g.poologasundarampillai@
>
>
  1. evelina.ametova@
  2. gavin.taylor.01@
  3. evangelos.papoutsellis@
  4. oriol.roche.15@
  5. alan.clarke@
  6. g.poologasundarampillai@
 

Working Group Meeting Agenda (19 November 2018)

Agenda; 19 November 2018
Line: 228 to 244
  Meet from 10:30 and setup AV with coffee/biscuits provide at RAL and Manchester locations.
Changed:
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  • 11:00 Minutes and Actions
  • 11:20 Plans for 2019-2020 "To be Approved" and Software Launch (release version 1.x)
>
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  • 11:00 Minutes and Actions
  • 11:20 Plans for 2019-2020 "To be Approved" and Software Launch (release version 1.x)
 
    • Overview of CIL and Flagship events
    • Request for wish-list items for future versions
    • Software grant for Erasmus student in Soton for work on TIGRE/CIL integration - £6k? - £14k?
Changed:
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    • BL - Multiple axes and tensor/vector tomography in CCPi code: additional resources requested
>
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    • BL - Multiple axes and tensor/vector tomography in CCPi code: additional resources requested
 
    • GD - Forward projection code request (EP/BL)
Changed:
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  • 11:35 Invited speaker on (10 mins each)
>
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  • 11:35 Invited speaker on (10 mins each)
 
    • Jay Warnett - WMG new facility
    • Bob Cernik - Colour bay facility at University of Manchester
    • Evangelos (Vaggelis) Papoutsellis - Reconstruction software development
Changed:
<
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  • 12:15 Review of Summer Associated Conferences: new cttee member requests
    • Process Tomography / ToScA (inc International - USA and Asia) / dXCT / RCaH "Advances" workshop EGUK September for 2019 and 2020
    • Joint PETMR activities and PETMR joint course at MIC in November 2019 at Manchester:
      • Workshop Proposal submitted "Synergistic multi-modal & multi-spectral image reconstruction: methods & software" Tuesday, 29/10/2019; Organising Committee (Provisional): William Lionheart, Martin Turner, Kris Thielemans, Claudia Prieto, David Atkinson, Charalampos Tsoumpas; Advisory Board (Provisional): Simon Arridge, Andrew Reader, Julian Matthews, Jeff Fessler, Cyprian Catana, Edoardo Pasca Contact Person: c.tsoumpas@leeds.ac.uk Expected Attendance: At least 200-250 people
    • Update: TPR/1 (TDW/4) /11 (XCT), Technical product realization (BSI, 389 Chiswick High Road, London W4 4AL)
  • 12:30 Update on International Review of CoSeC
    • Future grant networks and ... case studies (of networking)
    • Training review - DVC - second version but how to make open-source?
>
>
  • 12:15 Review of Summer Associated Conferences: new cttee member requests
    • Process Tomography / ToScA (inc International - USA and Asia) / dXCT / RCaH "Advances" workshop EGUK September for 2019 and 2020
    • Joint PETMR activities and PETMR joint course at MIC in November 2019 at Manchester:
      • Workshop Proposal submitted "Synergistic multi-modal & multi-spectral image reconstruction: methods & software" Tuesday, 29/10/2019; Organising Committee (Provisional): William Lionheart, Martin Turner, Kris Thielemans, Claudia Prieto, David Atkinson, Charalampos Tsoumpas; Advisory Board (Provisional): Simon Arridge, Andrew Reader, Julian Matthews, Jeff Fessler, Cyprian Catana, Edoardo Pasca Contact Person: c.tsoumpas@leeds.ac.uk Expected Attendance: At least 200-250 people
    • Update: TPR/1 (TDW/4) /11 (XCT), Technical product realization (BSI, 389 Chiswick High Road, London W4 4AL)
  • 12:30 Update on International Review of CoSeC
    • Future grant networks and ... case studies (of networking)
    • Training review - DVC - second version but how to make open-source?
 
  • 12:40 New networks and proposals
    • Small funds for ToScA USA approved - paper/presentation submitted
    • BSS Fellowship submitted (Brain Bay, October 2018)
Changed:
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    • SSI Fellowship role to be supported, November 2018 "HPC: SCARF18, Archer access: 'constructive critical champion' role."
    • Leverhulme visiting professor role at UoM
    • Industrial role in UoM with RAL?
    • Training course for programming Nikon CT machines - funds for travel to Swansea
  • 12:50 New Working Group members.
>
>
    • SSI Fellowship role to be supported, November 2018 "HPC: SCARF18, Archer access: 'constructive critical champion' role."
    • Leverhulme visiting professor role at UoM
    • Industrial role in UoM with RAL?
    • Training course for programming Nikon CT machines - funds for travel to Swansea
  • 12:50 New Working Group members.
 
  • 13:00 Access to IMAT and i12, i13, B24 and industrial grants.
  • 13:10 Administration
Changed:
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    • jiscmail lists and website content etc
  • AOB
>
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    • jiscmail lists and website content etc
  • AOB
 
  • Location for next WG at RAL with Fringe Meeting, 11 June 2019

1pm-2pm COMBINED Lunch available

Line: 266 to 282
 2pm-3:30pm Flagship round table meeting

Plans for 2019-2020 _To be Approved_

Changed:
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  1. Website, mailing lists, source code and data archives Ongoing
  2. Organise exec committee and working group meetings, as well as monthly show-and-tell sessions Ongoing
  3. Support current training courses and organise developer workshops. Assist in new proposal writing. Ongoing
  4. Working with CCPi Flagship team in improving Core Imaging Library (CIL) and integrating the codes from flagship into CIL. Ongoing
  5. Embed CCPi software into DAaS virtual machine to allow facilities users (DLS, ISIS) to perform analysis on their datasets from remote Ongoing
  6. Release updated version of Simpleflex segmentation algorithm developed together with Hamish Carr (Leeds) and his student. Distribute and collaborate with Diamond i12 staff to test the segmentation on real data Q2 2019
  7. Help to organise the main ToScA conference; September 2019 Q3 2019
  8. Embed lab based framework: UoM/ UoS/ UoW Q3 2019
  9. Collaboration: Working with Brian Bay (USA) on improving the digital volume correlation codes and distributing it to CCPi community Ongoing
  10. Case Studies: Three case studies will be undertaken with ISIS/Diamond and Universities Ongoing
  11. Code sharing with CCPPETMR Ongoing
>
>
  1. Website, mailing lists, source code and data archives Ongoing
  2. Organise exec committee and working group meetings, as well as monthly show-and-tell sessions Ongoing
  3. Support current training courses and organise developer workshops. Assist in new proposal writing. Ongoing
  4. Working with CCPi Flagship team in improving Core Imaging Library (CIL) and integrating the codes from flagship into CIL. Ongoing
  5. Embed CCPi software into DAaS virtual machine to allow facilities users (DLS, ISIS) to perform analysis on their datasets from remote Ongoing
  6. Release updated version of Simpleflex segmentation algorithm developed together with Hamish Carr (Leeds) and his student. Distribute and collaborate with Diamond i12 staff to test the segmentation on real data Q2 2019
  7. Help to organise the main ToScA conference; September 2019 Q3 2019
  8. Embed lab based framework: UoM/ UoS/ UoW Q3 2019
  9. Collaboration: Working with Brian Bay (USA) on improving the digital volume correlation codes and distributing it to CCPi community Ongoing
  10. Case Studies: Three case studies will be undertaken with ISIS/Diamond and Universities Ongoing
  11. Code sharing with CCPPETMR Ongoing
 
  1. Optional: benchmark the core forward and backprojection code in CCPi - Barry Searle's modification of David Szotten's Jacob's rays - using MPI

Please email to attend at Manchester or RAL and confirm catering.

  • SSI fellowship application
Changed:
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  • ATI fellowship application
  • special issue paper (DK)
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  • ATI fellowship application
  • special issue paper (DK)
 
  • Roy Regallies and Phil Manning: ICAL / TL ... YXLON progress
Changed:
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  • PhD iCASE - (TL) 3D targets for errors; turbine blade; corroded pipes EDF; F1 engine block.
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  • PhD iCASE - (TL) 3D targets for errors; turbine blade; corroded pipes EDF; F1 engine block.
  Resources:
Changed:
<
<
  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on code C01
  • SCARF18 - should be open for SCD staff
  • Location for papers on ccpi.ac.uk - including beamhardening: Docs: https://ccpi-core-imaging-library-cil.readthedocs.io/en/latest/beamhardening.html#downloading-and-running-the-software and paper at: https://authors.elsevier.com/sd/article/S2352711018300360
>
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  As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.
Line: 311 to 327
 1. Network Activities

2. CIL-Core development: linking with Flagship software + papers etc

Changed:
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  Including DVC code being ported into CIL

3. New Recruits

Changed:
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  Including Machine Learning summer students
Changed:
<
<
4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm
>
>
4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm
  5. Contacts with Thomas Blumensath from Southampton for contributing his parallel reconstruction alg
Line: 332 to 348
 
  • WMG strategic equipment: been awarded and details at Governance Group meeing Jan 2019 (MT/CCPi has been invited)
  • 2 x summer students in ML - presentation for December (lunch-and-learn planned)
Changed:
<
<
  • SAXS funding - Bill Lionhear (accept to visit Cambridge / Oxford and RAL to star project proposal - BL/MT to coordainate)
>
>
  • SAXS funding - Bill Lionhear (accept to visit Cambridge / Oxford and RAL to star project proposal - BL/MT to coordainate)
 
  • B24 funding / staff request (data through Mark Basham to be coordainate - DK/EP)
Changed:
<
<
  • Parmesh request to visit Swansea and USA !ToScA (Agreed to travel and represeat CCPi)
>
>
  • Parmesh request to visit Swansea and USA ToScA (Agreed to travel and represeat CCPi)
 
  • 22 June 2018 Meeting at Huddersfield University and planning for dXCT 2019 and 2020 (Royce to have a stand at 2019 event)
  • Colour Bay meetings (started by BC and Flaghip to be represented)
Line: 365 to 381
  CCPi conferences and workshops: Summer 2018
Changed:
<
<
  • Advanced Xray Imaging Workshop June 15 2018
  • Fringe meeting June 14 2018: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur
  • dimension XCT conference at Nottingham: July 2018
  • !ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
>
>
  • Advanced Xray Imaging Workshop June 15 2018
  • Fringe meeting June 14 2018: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur
  • dimension XCT conference at Nottingham: July 2018
  • ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)
  2. CIL-Core development: linking with Flagship software
Line: 382 to 398
  Papers etc:
Changed:
<
<
  • !TomoPhantom software and paper: https://github.com/dkazanc/TomoPhantom
  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
>
>
 
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop

3. New Recruits

Changed:
<
<
  • Flagship posts x2 been offered (possible start dates 1 Nov 2018 and 1 Dec 2018)
  • Core CCPi role x1.5: New Recruit (apps by 21 October 2018; so potentially start in Jan 2019); Tomas Kulhanek (based at DL) to join (mid Oct - end Dec 2018) and work on continuous integration and also test-cases at Manchester (contact Parmesh Gajjar and Tristan Lowe)
>
>
  • Flagship posts x2 been offered (possible start dates 1 Nov 2018 and 1 Dec 2018)
  • Core CCPi role x1.5: New Recruit (apps by 21 October 2018; so potentially start in Jan 2019); Tomas Kulhanek (based at DL) to join (mid Oct - end Dec 2018) and work on continuous integration and also test-cases at Manchester (contact Parmesh Gajjar and Tristan Lowe)
  4. AOB

  • Website and email list (review by EP/MT)
Changed:
<
<
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
>
>
  • International Review complete for CoSeC and informal monthly events (DL and RAL) as well as away-days (30 March-1 April 2018; 2 October)
 
Line: 404 to 420
  Training / Seminar:
Changed:
<
<
  • Workshop ‘Fibre Reinforced Composites: X-ray Imaging and Advanced Fibre Tracking’ that will take place at the Henry Moseley X-ray Imaging Facility on Tuesday 15th May 2018 (34 att)
  • 17 May 2018, 10am-12noon Avizo hands-on session with FEI at RAL
  • 4 July 2018 Seminar at RAL on Digital Volume Correlation by Prof. Brian Bay (Oregon State University)
  • 6 July 2018, 9:30am pre-coffee talk - Remote Visualisation and Analysis of Tomographic Data - Providing Near Data Analysis Environments and Visualisation for Diamond Data; Richard Smith
  • Regular Manchester Avizo courses; 6-7 March 2018; 5-6 June 2018
>
>
  • Workshop ‘Fibre Reinforced Composites: X-ray Imaging and Advanced Fibre Tracking’ that will take place at the Henry Moseley X-ray Imaging Facility on Tuesday 15th May 2018 (34 att)
  • 17 May 2018, 10am-12noon Avizo hands-on session with FEI at RAL
  • 4 July 2018 Seminar at RAL on Digital Volume Correlation by Prof. Brian Bay (Oregon State University)
  • 6 July 2018, 9:30am pre-coffee talk - Remote Visualisation and Analysis of Tomographic Data - Providing Near Data Analysis Environments and Visualisation for Diamond Data; Richard Smith
  • Regular Manchester Avizo courses; 6-7 March 2018; 5-6 June 2018
  Other items:
Changed:
<
<
  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
>
>
 
  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

Changed:
<
<
  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
>
>
  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
 
  • Bath presentation (joint NPL project)
Changed:
<
<
  • Future Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
  • New BSS Fellowship aplication with BB
>
>
  • Future Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
  • New BSS Fellowship aplication with BB
  Case Studies:
Changed:
<
<
  • PE activities
  • beam hardening
  • quantifucationn - porosity
  • parts of CIL
  • ULTRA integration
>
>
  • PE activities
  • beam hardening
  • quantifucationn - porosity
  • parts of CIL
  • ULTRA integration
 

Summer 2018 International-interim revirew items

Resources:

Changed:
<
<
  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on C01 TODO
  • SCARF18 - should be open for SCD runs parallel in principle.
>
>
  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on C01 TODO
  • SCARF18 - should be open for SCD runs parallel in principle.
  Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
Changed:
<
<
  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
>
>
  1. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
 
  1. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  2. Are you involved in any eCSE projects (please provide details)? No
  3. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
Line: 463 to 479
  Interview points:
Changed:
<
<
  • Examples of SLA impact specifically
  • Any details of further funding leveraged off the SLA support
>
>
  • Examples of SLA impact specifically
  • Any details of further funding leveraged off the SLA support
  Options for future (from Steering Panel; June 2018)
Line: 478 to 494
  Other points:
Changed:
<
<
  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)
>
>
 
Line: 488 to 504
  Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 406 subscribers; 46 new members since May 2018
Changed:
<
<
  1. neil.o'brien@
  2. K.Alsop@
  3. alexander.kao@
  4. c.rossides@
  5. v.fernandez@
  6. swhitbread@
  7. 445305@
  8. oliver.larkin@
  9. ch230@
  10. paul.gunning@
  11. dlatron1@
  12. ilias.kounatidis@
  13. fabio.vittoria.12@
  14. saldridge@
  15. 973879@
  16. christopher.thornton@
  17. k.r.hallam@
  18. jflynn@
  19. strgx@
  20. Brian.Bay@
  21. kalpani.vitharana@
  22. chris.morris@
  23. tomas.kulhanek@
  24. ian.belding@
  25. tohru.araki@
  26. ewelina.kosior@
  27. malte.storm@
  28. sultan.mahmood@
  29. seamus.murphy@
  30. dan.symes@
  31. robert.weatherup@
  32. antoine.cornet@
  33. john.flynn@
  34. j.mathew@
  35. ander.biguri@
  36. i.s.charlwood@
  37. r.johnston@
  38. ben.morgan@
  39. naeem.desai@
  40. tom.etheridge@
  41. Ira.Dekker@
  42. Christopher.Price@
  43. Ian.Nicholson@
  44. Elizabeth.Surrey@
  45. rob.akers@
  46. daniel.pooley@
>
>
  1. neil.o'brien@
  2. K.Alsop@
  3. alexander.kao@
  4. c.rossides@
  5. v.fernandez@
  6. swhitbread@
  7. 445305@
  8. oliver.larkin@
  9. ch230@
  10. paul.gunning@
  11. dlatron1@
  12. ilias.kounatidis@
  13. fabio.vittoria.12@
  14. saldridge@
  15. 973879@
  16. christopher.thornton@
  17. k.r.hallam@
  18. jflynn@
  19. strgx@
  20. Brian.Bay@
  21. kalpani.vitharana@
  22. chris.morris@
  23. tomas.kulhanek@
  24. ian.belding@
  25. tohru.araki@
  26. ewelina.kosior@
  27. malte.storm@
  28. sultan.mahmood@
  29. seamus.murphy@
  30. dan.symes@
  31. robert.weatherup@
  32. antoine.cornet@
  33. john.flynn@
  34. j.mathew@
  35. ander.biguri@
  36. i.s.charlwood@
  37. r.johnston@
  38. ben.morgan@
  39. naeem.desai@
  40. tom.etheridge@
  41. Ira.Dekker@
  42. Christopher.Price@
  43. Ian.Nicholson@
  44. Elizabeth.Surrey@
  45. rob.akers@
  46. daniel.pooley@
 

CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship

Changed:
<
<
Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
>
>
Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.
  Network targets: # of people / projects to gain impact items - What kind of code and bids: we should be preparing, in terms of best impacts
Line: 548 to 564
  Meet from 10:30 and setup AV.
Changed:
<
<
>
>
 
    • Overview of CIL and Flagship events
    • Request for wish-list items for v1.1
Changed:
<
<
  • 11:35:12:15 Invited speaker on (10 mins each)...
    • Chris Race on ML and AI in Materials Science
    • Jakob Jorgensen and Parmesh Gajjar - Laminography reconstruction
    • Alan Kyffin regarding Anvil/repository
    • Brain Bay / Catherine Disney
  • 12:15:12:30 Associated Conferences:
    • EGUK September 2019 - Visual Analytics course with CECAM, at Daresbury Labs
    • Join course with PETMR at MIC in November 2019 at Manchester
>
>
  • 11:35:12:15 Invited speaker on (10 mins each)...
    • Chris Race on ML and AI in Materials Science
    • Jakob Jorgensen and Parmesh Gajjar - Laminography reconstruction
    • Alan Kyffin regarding Anvil/repository
    • Brain Bay / Catherine Disney
  • 12:15:12:30 Associated Conferences:
    • EGUK September 2019 - Visual Analytics course with CECAM, at Daresbury Labs
    • Join course with PETMR at MIC in November 2019 at Manchester
 
    • dXCT - planning for 2019 (Huddersfield?) and 2020 (Manchester?)
    • ToScA 2018 and USA in 2019
Changed:
<
<
  • 12:30-12:40 Update on International Review of CoSeC
    • SLA only: 12 June 2018 draft - 12 July 2018 SLA steering cttee meeting 20 July 2018 updated draft
    • Likely submission on 20 August 2018 with Review on 15 October 2018
    • May require posters, interviews and
    • ... case studies (of networking)
>
>
  • 12:30-12:40 Update on International Review of CoSeC
    • SLA only: 12 June 2018 draft - 12 July 2018 SLA steering cttee meeting 20 July 2018 updated draft
    • Likely submission on 20 August 2018 with Review on 15 October 2018
    • May require posters, interviews and
    • ... case studies (of networking)
 
  • 12:40 New networks and proposals
    • Small funds for Llion Evans (lunch),22 May 2018 "Virtual Qualification: First Stakeholder Meeting"
    • Small funds to support for project connected to more efficient ray-tracing techniques. Bill Lionheart
    • BILAT USA 4.0 Workshop on US Funding Opportunities for European Researchers - future USA collab
Changed:
<
<
  • 12:50 New Working Group members - NPL / Neil Bourne / ...
>
>
  • 12:50 New Working Group members - NPL / Neil Bourne / ...
 
  • 13:00 Access to IMAT and i13
  • 13:10 Administration
    • distibution jiscmail lists
Line: 619 to 635
  - Advanced Xray Imaging Workshop June 15 2018: speakers; ACTION Requested funds for travel for speakers (same as 2017) FRINGE meeting being planned for June 14, 2018
Changed:
<
<
  • ‘Revealing defect dynamics in laser additive manufacturing by in situ and operando X-ray imaging’, Alex Leung, University of Manchester
  • ‘Digital Volume Correlation: Progress and Challenges’, Francois Hild, University Paris-Saclay
  • ‘Title TBA’ (topic likely to be around image based modelling and integrating automation into workflow), Llion Evans, Swansea University
  • ‘Title TBA’ (topic likely to be tomography of porous systems), Maxime Moreau, French Institute of Petroleum
  • ‘4D tomography applied to magnetic systems’, Kate Dobson, University of Durham
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
>
>
  • ‘Revealing defect dynamics in laser additive manufacturing by in situ and operando X-ray imaging’, Alex Leung, University of Manchester
  • ‘Digital Volume Correlation: Progress and Challenges’, Francois Hild, University Paris-Saclay
  • ‘Title TBA’ (topic likely to be around image based modelling and integrating automation into workflow), Llion Evans, Swansea University
  • ‘Title TBA’ (topic likely to be tomography of porous systems), Maxime Moreau, French Institute of Petroleum
  • ‘4D tomography applied to magnetic systems’, Kate Dobson, University of Durham
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader
  - Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested
Line: 638 to 654
  Extra CCPi supported meetings:
Changed:
<
<
- EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering at Swansea University in the UK. Co-Director of the £10M Advanced Imaging of Materials (AIM) facility at Swansea, of the £13.7M Materials and Manufacturing Academy for postgraduate training, and the STFC Regional Beamline-Bridging Facility. Founder and Director of the Research as Art awards, which have reached over 50 million people worldwide since 2009, A Software Sustainability Institute Fellow, and a previous British Science Association Media Fellow at Nature) "Title: Visualisation in Microscopy – making sense of the invisible world in 3D"
>
>
- EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering at Swansea University in the UK. Co-Director of the £10M Advanced Imaging of Materials (AIM) facility at Swansea, of the £13.7M Materials and Manufacturing Academy for postgraduate training, and the STFC Regional Beamline-Bridging Facility. Founder and Director of the Research as Art awards, which have reached over 50 million people worldwide since 2009, A Software Sustainability Institute Fellow, and a previous British Science Association Media Fellow at Nature) "Title: Visualisation in Microscopy – making sense of the invisible world in 3D"
  - 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
Line: 650 to 666
 
  • CIL Reconstruction Framework as discussed on 18/12/17.
    • i. Planning of framework done in January 2018
    • ii. Coding sprint (with Flagship) in March 2018
Changed:
<
<
    • iii. The code is about to be released open source and contains a framework to quickly develop novel reconstruction algorithms. Readers for Xtek and NeXus.
>
>
    • iii. The code is about to be released open source and contains a framework to quickly develop novel reconstruction algorithms. Readers for Xtek and NeXus.
 
    • iv. Working at Sophiabeads dataset as benchmark
  • A weekly t-con with core team and flagship team is ongoing on Tuesdays 10:30am (open to anyone - started 18 December 2017)

Segmentation:

  • Simpleflex: Working with Prof. Hamish Carr and student to add functionality and quantification tools on the segmented isosurfaces
Changed:
<
<
  • !SurVos: maintain a this segmenting tool developed by Diamond and Nottingham. Created a windows binary for the use of Diamond i14. Currently we maintain this tool because Diamond doesn’t have resources. Do we?
>
>
  • SurVos: maintain a this segmenting tool developed by Diamond and Nottingham. Created a windows binary for the use of Diamond i14. Currently we maintain this tool because Diamond doesn’t have resources. Do we?
  User engagement:
Changed:
<
<
  • Simpleflex segmentation: we have 3 main contacts: Dr. Robert Atwood (diamond i12, I believe), Dr. Nolwenn !LeGall (Manchester working @ Diamond), Prof. Jawei Mi (Hull). Edo is working together with the scientists to guide them using the algorithm. When needed/possible, new functionality is added. The obvious endpoint is to work with the SAVU team to distribute the Simpleflex segmentation within their framework, as both Diamond and Hull have it.
>
>
  • Simpleflex segmentation: we have 3 main contacts: Dr. Robert Atwood (diamond i12, I believe), Dr. Nolwenn LeGall (Manchester working @ Diamond), Prof. Jawei Mi (Hull). Edo is working together with the scientists to guide them using the algorithm. When needed/possible, new functionality is added. The obvious endpoint is to work with the SAVU team to distribute the Simpleflex segmentation within their framework, as both Diamond and Hull have it.
 
  • Nick Brierly from MTC who expressed interest in CCPi code, has bought a commercial product.

Networking:

Changed:
<
<
  • Strengthened bonds between CCPi and CCPPETMR by sharing code/solutions. CCPi has adhered to the CCPPETMR naming and coding convention in the development of the Reconstruction Framework, so that it could be easily taken by the CCPPETMR. There is an active discussion between the CCP’s about the definition of the objective function for the optimization problem, for which CCPi core and flagship teams have found one solution.
>
>
  • Strengthened bonds between CCPi and CCPPETMR by sharing code/solutions. CCPi has adhered to the CCPPETMR naming and coding convention in the development of the Reconstruction Framework, so that it could be easily taken by the CCPPETMR. There is an active discussion between the CCP’s about the definition of the objective function for the optimization problem, for which CCPi core and flagship teams have found one solution.
  Extras for Flagship specific development:
Line: 687 to 703
  Extra:
Changed:
<
<
  • Liverpool issue with DLS data (request from Robert Atwood): automated data cropping
  • Monitoring data transfer flow from DLS to Soton.
  • ...
>
>
  • Liverpool issue with DLS data (request from Robert Atwood): automated data cropping
  • Monitoring data transfer flow from DLS to Soton.
  • ...
  3. New Management at SCD/STFC
Changed:
<
<
  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
>
>
  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.
  4. AOB
Changed:
<
<
  • International Review for CoSeC
  • Add software fellows to Working Group list as associate members: Parmesh Gajjar (Manchester, CCPi) and Richard Brown (UCL, CCPPETMR)...
>
>
  • International Review for CoSeC
  • Add software fellows to Working Group list as associate members: Parmesh Gajjar (Manchester, CCPi) and Richard Brown (UCL, CCPPETMR)...
  Points Raised with more details: from November 2017 meeting:

Visitors/Fellowships awarded:

Changed:
<
<
  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
>
>
  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM): Outcome: software to be integrated with Flagship.
  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv
  Training / Seminar:
Changed:
<
<
  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
>
>
  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
 
Changed:
<
<
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
>
>
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;
  Future Ideas/Invitations:
Changed:
<
<
  • NPL to talk at Manchester - 8 May 2018 ACCEPTED
>
>
  • NPL to talk at Manchester - 8 May 2018 ACCEPTED
 
  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
Changed:
<
<
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
  • ... Nick Brierley (the-MTC) invited to Manchester October 2018 ACCEPTED
  • CCPi joint workshop EY/PW on various modes - see possibly Fringe event of CECAM 2019 event
  • Bath presentation (joint NPL project)
  • ...
  • Fellowship Llion Evans to be invited to Fringe: ACCEPTED
  • Martyn Winn invited to Fringe
  • CCPPETMR Richard invited to Fringe
  • ...
>
>
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
  • ... Nick Brierley (the-MTC) invited to Manchester October 2018 ACCEPTED
  • CCPi joint workshop EY/PW on various modes - see possibly Fringe event of CECAM 2019 event
  • Bath presentation (joint NPL project)
  • ...
  • Fellowship Llion Evans to be invited to Fringe: ACCEPTED
  • Martyn Winn invited to Fringe
  • CCPPETMR Richard invited to Fringe
  • ...
  More ideas welcome ...
Changed:
<
<
  • Fringe meeting for Advances in Xray Imaging Workshop - ideas of topics welcome.
  • 17-19 January code sharing and 5-7 March 2018 Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
>
>
  • Fringe meeting for Advances in Xray Imaging Workshop - ideas of topics welcome.
  • 17-19 January code sharing and 5-7 March 2018 Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
  Case Studies:
Changed:
<
<
  • "CCP Chairs to pass on existing case studies" note need for International Review of CCPs in Summer 2018
  • PE activities
  • beam hardening
  • quantifucationn - porosity
  • parts of CIL
  • ULTRA integration
>
>
  • "CCP Chairs to pass on existing case studies" note need for International Review of CCPs in Summer 2018
  • PE activities
  • beam hardening
  • quantifucationn - porosity
  • parts of CIL
  • ULTRA integration
  Other items
Line: 789 to 805
  Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship
Changed:
<
<
Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
>
>
Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.
  Network targets: # of people / projects impact items
Line: 803 to 819
  Session 1:
Changed:
<
<
  • (30 mins) Minutes and Actions (see list below)
>
>
  • (30 mins) Minutes and Actions (see list below)
 
  • (30 mins) CoSeC Updates
Changed:
<
<
    • Licensing – SN/MT (5mins)
>
>
    • Licensing – SN/MT (5mins)
 
    • CIL Work plan and priorities -- SN/EP (15mins)
Changed:
<
<
      • Brian Bray – SN
      • Mark Basham – SAVU updates + Survos + users (5mins)
>
>
      • Brian Bray – SN
      • Mark Basham – SAVU updates + Survos + users (5mins)
 
    • Case Study: (10mins)
Changed:
<
<
      • Segmentation using simpleflex – EP
      • Root dataset with missing projections – Genoveva/SN
>
>
      • Segmentation using simpleflex – EP
      • Root dataset with missing projections – Genoveva/SN
 
  • (5 mins) Events and Training Updates
Changed:
<
<
  • (10 mins) FISTA Reconstruction – EP/Daniil
  • (15 mins) CCPi Flagship Update – Daniil/Jacob
>
>
  • (10 mins) FISTA Reconstruction – EP/Daniil
  • (15 mins) CCPi Flagship Update – Daniil/Jacob
  Lunch:
Line: 822 to 838
 
  • (15 mins) Pre-processing Imaging techniques (Nghia Vo)
  • (15 mins) Thomas Blumensath, Southampton University (TB)
Changed:
<
<
  • (15 mins) Paul Quinn – DLS I14 new techniques and Updates
>
>
  • (15 mins) Paul Quinn – DLS I14 new techniques and Updates
 
  • (5 mins) US/UK collaboration update (MT)
  • (10 mins) actions + further discussion
  • AOB

ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf

Changed:
<
<
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
  • DONE - PW to provide contact information to NV for users on I13 with image processing issues.
  • DONE - Submit ParaView paper to EGUK (MT) also paper accepted on 12 DOF input devices for Tomography.
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
  • ...
  • TODO GD and BL to discuss editing new Phil Trans issue on reconstruction. GD/BL BL putting together a list (October 2017).
  • TODO Updated proposal for joint CCPi/CCP workshop MT/BL/KT ON HOLD
>
>
  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
  • DONE - PW to provide contact information to NV for users on I13 with image processing issues.
  • DONE - Submit ParaView paper to EGUK (MT) also paper accepted on 12 DOF input devices for Tomography.
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
  • ...
  • TODO GD and BL to discuss editing new Phil Trans issue on reconstruction. GD/BL BL putting together a list (October 2017).
  • TODO Updated proposal for joint CCPi/CCP workshop MT/BL/KT ON HOLD
 

Future Activities and requests for funds:

  • Update on a CPC paper proposal for 2019
Changed:
<
<
  • Avizo-Amira update on project collaborations
>
>
  • Avizo-Amira update on project collaborations
 
  • Nick Brierley - MTC group - project: software-show-and-tell for 2018
  • Proposed visit - Paul Bills (Hudds)
  • Workshop Support; February 2018 a 1 day event for 20-30 UK people to meet who contribute to the ParaFEM software - linked to image-based modelling. (Lee Margetts) Request £1k for food and visiits regarding CT priorities.
Line: 866 to 882
 
  • Grants Submitted: EU COST project, 7 September 2017 (April 2018) EPSRC UK-USA collaboration, August 2017
  • ...
Changed:
<
<
Items from Exec Meeting (October 2017) to take forward: created a Weekly tech meeting on Monday – 3:30pm for the Core CCPi and MT to focus on impact items.
>
>
Items from Exec Meeting (October 2017) to take forward: created a Weekly tech meeting on Monday – 3:30pm for the Core CCPi and MT to focus on impact items.
 
  • PW has proposed that the core team should prepare at least one User case study for each component of the CIL
Changed:
<
<
  • Prepare the "work"-plan for CCPi “Development and Engagement Plans”
>
>
  • Prepare the "work"-plan for CCPi “Development and Engagement Plans”
 
  • EP informed that he is working with Robert Atwood in getting data to segmentation with CIL and would be writing this work as part of a User case study report
  • A decision has to be made about what type of software licensing under which CIL code should be released
Changed:
<
<
  • Parmesh Gajjar wanting to setup a training session for “Nikon machine hacking”
>
>
  • Parmesh Gajjar wanting to setup a training session for “Nikon machine hacking”
 
  • MT has mentioned collaboration with Nick Brierley in MTC group
  • PW to link up EP with Jacob on sparse beads paper (DONE)
Changed:
<
<
  • MT to write a summary for SCD newsletter on CCPi activities
>
>
  • MT to write a summary for SCD newsletter on CCPi activities
 
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day

General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)

Line: 894 to 910
  Main Meetings:
Changed:
<
<
  • ToScA 6-8 September 2017
  • dXCT 13 July 2017 (150 att)
  • Techy RAL session plus Fringe event: 13 June 2017 and 12 June 2017
>
>
  • ToScA 6-8 September 2017
  • dXCT 13 July 2017 (150 att)
  • Techy RAL session plus Fringe event: 13 June 2017 and 12 June 2017
  Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 369 subscribers; 45 new members since July 2017
Line: 963 to 979
  Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm
Changed:
<
<
  • Approval of past six months activities (SN)
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
      • addition scan at DLS of BSI 4/4/1 samples
    • CCPi have letters of support for fellowship applications; EPSRC Manufacturing Fellowship/ EPSRC RSE II x2 / Ser Cymru Fellowship; and a tomiz.org proposal with kitware - to maintain developers.
    • EU COST links and future proposal (19 June 2017) OC-2016-2-21631 'Tomography Across Modalities and Scales'
  • Flagship update (DK/JJ)
  • Software plan / coding milestones (SN)
  • New actions / milestones
  • Web-site
  • Future meetings dXCT - NPL/BSI @WMG and ToScA @Portsmouth
  • Update from 'sister' CCPPETMR network (KT)
  • Short Talks:
    • Nghio Vo (DLS)
    • Srikanth Nagella - CIL (CCPi Core)
>
>
  • Approval of past six months activities (SN)
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
      • addition scan at DLS of BSI 4/4/1 samples
    • CCPi have letters of support for fellowship applications; EPSRC Manufacturing Fellowship/ EPSRC RSE II x2 / Ser Cymru Fellowship; and a tomiz.org proposal with kitware - to maintain developers.
    • EU COST links and future proposal (19 June 2017) OC-2016-2-21631 'Tomography Across Modalities and Scales'
  • Flagship update (DK/JJ)
  • Software plan / coding milestones (SN)
  • New actions / milestones
  • Web-site
  • Future meetings dXCT - NPL/BSI @WMG and ToScA @Portsmouth
  • Update from 'sister' CCPPETMR network (KT)
  • Short Talks:
    • Nghio Vo (DLS)
    • Srikanth Nagella - CIL (CCPi Core)
 
  • Review mid-term forecast targets
  • AOB:
    • Data transfer, "results from the RAL perfSONAR host to Manchester are around 3 Gbps and about 5 Gbps inbound to RAL"
Line: 993 to 1009
 Lunchtime 1pm-2pm Food (for 22) with a demonstration of Volume/Surface Tomography Visualisation with VR - Unity software.

  • Adative manufacturing - discussion - side meeting with Mike Curtuis-Rouse: 1pm
Changed:
<
<
  • ISIS / IMAT - next stage - side meeting with Genoveva Burca: 2pm
>
>
  • ISIS / IMAT - next stage - side meeting with Genoveva Burca: 2pm
  Fringe Agenda: 2:30pm-5pm
Changed:
<
<
  • The Future of XCT - 'unusual' code solutions
>
>
  • The Future of XCT - 'unusual' code solutions
 
    • Flagship grant for Multi Channel CT and missing wedge/ poor data reconstruction (DK/JJ)
Changed:
<
<
    • Sam Cooper, TauFactor tomography tool to calculate toruosity factor, volume fractions, etc
    • Darren Batey, Beamline I13, Diamond Light Source ‘Ptychography: Looking beyond the lens’
    • Tim Burnett, Henry Moseley X-ray Imaging Facility, University of Manchester ‘Multiscale 3D microstructure analysis with site specific targeting through correlation of X-ray CT and FIB-SEM serial sectioning'
    • Andy King, Soleil 'Combining tomography and diffraction at the PSICHE beamline, SOLEIL'
    • Margie Olbinado, ID19, ESRF ‘Million frames per second hard X-ray phase contrast imaging using synchrotron
  • The EPSRC XCT Roadmap outline and discussion (MT lead)
    • link to BSI standards
    • what would you do "future vision"
      • "supporting suitable and well rationalised technique-based roadmaps e.g. NMR spectroscopy..."
      • "current UK capital infrastructure ... which in turn may lead to more and/or better equipment sharing"
      • "... will have community buy-in; demonstrated through applicants taking it into consideration"
  • Unusual events as well as Coffee and Tea from 2:30pm (for 22).
>
>
    • Sam Cooper, TauFactor tomography tool to calculate toruosity factor, volume fractions, etc
    • Darren Batey, Beamline I13, Diamond Light Source ‘Ptychography: Looking beyond the lens’
    • Tim Burnett, Henry Moseley X-ray Imaging Facility, University of Manchester ‘Multiscale 3D microstructure analysis with site specific targeting through correlation of X-ray CT and FIB-SEM serial sectioning'
    • Andy King, Soleil 'Combining tomography and diffraction at the PSICHE beamline, SOLEIL'
    • Margie Olbinado, ID19, ESRF ‘Million frames per second hard X-ray phase contrast imaging using synchrotron
  • The EPSRC XCT Roadmap outline and discussion (MT lead)
    • link to BSI standards
    • what would you do "future vision"
      • "supporting suitable and well rationalised technique-based roadmaps e.g. NMR spectroscopy..."
      • "current UK capital infrastructure ... which in turn may lead to more and/or better equipment sharing"
      • "... will have community buy-in; demonstrated through applicants taking it into consideration"
  • Unusual events as well as Coffee and Tea from 2:30pm (for 22).
  Links: current EPSRC equipment Roadmap:
Changed:
<
<
>
>
  https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/

Networking and Funding Activities: December 2016 - May 2017

Changed:
<
<
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
>
>
  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
 
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
Line: 1034 to 1050
 
  • Training:
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
Changed:
<
<
    • Workshop on !SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
>
>
    • Workshop on SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
 
Changed:
<
<
  • Papers etc:
>
>
  • Papers etc:
 
    • Video usage on CCPi youtube channel in total is: 8,299 (51+63+67+81+109+251+7109+338+230) and 19 touchscreen examples exist (1x cfd, 10x3d models, 6xvideos, 2xmri models).
    • Data sets on archive: (one on dropbox - needs moving to zenodo); (new sparse-dataset; and two new links from Llion Evans)
Line: 1057 to 1073
  Items:
Changed:
<
<
  • CIL code from Nghia Vo (Action SN to arrange meetings)
  • Trip for Russell Garwood to meet ISIS/IMAT (Action MT to coordinate) also meet DK regarding flgship rtest data sets
>
>
  • CIL code from Nghia Vo (Action SN to arrange meetings)
  • Trip for Russell Garwood to meet ISIS/IMAT (Action MT to coordinate) also meet DK regarding flgship rtest data sets
 

Appendix C: details of events December 2016 - May 2017

Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 326 subscribers; 25 new members since December 2016 (plus 21 in June 2017, so far)

Changed:
<
<
  1. lyons@
  2. edoardo.pasca@
  3. llion.evans@
  4. peter.woolliams@
  5. michael.mccarthy.x@
  6. richard.watson@
  7. gc19@
  8. A.Attridge@
  9. p.j.bills@
  10. ralf.ziesche.16@
  11. lin.ma@
  12. hgliu@
  13. Suren.Chilingaryan@
  14. nicholas.jerome@
  15. dgursoy@
  16. c.heinzl@
  17. anders.kaestner@
  18. imanol.luengo@
  19. erica.yang@
  20. malte.ogurreck@
  21. silvia.cipiccia@
  22. a.bhartiya@
  23. liye.yan@
  24. shixiang.zhao@
  25. michele.darrow@
>
>
  1. lyons@
  2. edoardo.pasca@
  3. llion.evans@
  4. peter.woolliams@
  5. michael.mccarthy.x@
  6. richard.watson@
  7. gc19@
  8. A.Attridge@
  9. p.j.bills@
  10. ralf.ziesche.16@
  11. lin.ma@
  12. hgliu@
  13. Suren.Chilingaryan@
  14. nicholas.jerome@
  15. dgursoy@
  16. c.heinzl@
  17. anders.kaestner@
  18. imanol.luengo@
  19. erica.yang@
  20. malte.ogurreck@
  21. silvia.cipiccia@
  22. a.bhartiya@
  23. liye.yan@
  24. shixiang.zhao@
  25. michele.darrow@
 

Line: 1097 to 1113
 

CCPi Exec and Working Group meeting November 2016

Changed:
<
<
AGENDA Items for Exec Meeting 7 November 2016, 12:30pm – 2pm: agenda then Working Group meeting 21 November 2016, 10am-12:30pm
>
>
AGENDA Items for Exec Meeting 7 November 2016, 12:30pm – 2pm: agenda then Working Group meeting 21 November 2016, 10am-12:30pm
 
  • Approval of past six months activities
  • Exchanges
Line: 1108 to 1124
 
  • Web-site
  • Future meetings
  • Short Talks:
Changed:
<
<
    • Automated Testing Service Presentation - current work and future possibilities (RF)
    • Update on Beam Hardening (RF)
    • Update from CCP WSI organisation - fluid flow development (RF)
  • AOB
    • Advanced Radiotherapy Network+: Sandpits and PhD studentships
>
>
    • Automated Testing Service Presentation - current work and future possibilities (RF)
    • Update on Beam Hardening (RF)
    • Update from CCP WSI organisation - fluid flow development (RF)
  • AOB
    • Advanced Radiotherapy Network+: Sandpits and PhD studentships
  Extras:
Line: 1128 to 1144
 

Networking and funding activities:

  • There have been eight visitor exchanges as short-term fellows receiving small amounts of travel/subsistence money.
Changed:
<
<
  • One STFC summer student producing an updated Drishti/Prayog manual (zechang.xu) emphasis for ISIS/IMAT –launch 10 Oct – funded by ISIS.
  • Two UoM summer students carried out spiral reconstruction - about three months money requested (Moe, Yngve M.; Lloyd, Ryan) – funded by CCPi.
>
>
  • One STFC summer student producing an updated Drishti/Prayog manual (zechang.xu) emphasis for ISIS/IMAT –launch 10 Oct – funded by ISIS.
  • Two UoM summer students carried out spiral reconstruction - about three months money requested (Moe, Yngve M.; Lloyd, Ryan) – funded by CCPi.
 
  • Six seminars (software show-and-tells) events and ToScA organisation (included seven posters and a talk)
  • Five Public Engagement events (including the Manchester Science Festival at end of this month)
  • Link/advertise six training courses, for materials science visualisation.
Line: 1155 to 1171
 
  1. Add quantitative code examples from the community
  2. Add pre-processing stages inc. beamhardening correction experiments at DLS.
  3. Organise the main ToScA conference; September 2016
Changed:
<
<
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
>
>
  1. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)
  2. Optional: Optimise OpenCL projection algorithms.
 
Changed:
<
<
We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
>
>
We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/
  Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.
Line: 1167 to 1183
 CoI / PI / Working Group support is to be requested to guide in this effort:

  • Project proposal with Drishti (Ajay Limaye) and DLS (Mark Basham) being planned
Changed:
<
<
  • Project linking TIGRE with Bill Lionheart’s spiral reconstruction code
>
>
  • Project linking TIGRE with Bill Lionheart’s spiral reconstruction code
 
  • Project MIRAN code with CCPi developers (NE-Scientific - Andrea Borsic)
  • Software hacking the Nikon X-ray system (Parmesh Gajjar and Andrew Ramsey)
Changed:
<
<
  • Software linking the original Valeriy Titarenko’s reconstruction code to have a CCPi archive
>
>
  • Software linking the original Valeriy Titarenko’s reconstruction code to have a CCPi archive
 
  • Royal Society special issue: next one
  • New IoP Journal update (~March 2017)
  • ... and links with ToScA sponsors: RMS
Changed:
<
<
  • Workshop: “Quant Across Scales - Link to CCP5 and CCP-EM” (John Purton, Martyn Winn, etc)
>
>
  • Workshop: “Quant Across Scales - Link to CCP5 and CCP-EM” (John Purton, Martyn Winn, etc)
 
  • Rich Tomography proposal (Christopher Egen, Bob Cernic, Daniil Kazantsev etc)
  • ... link to S-J C and MT for sections
Changed:
<
<
  • CECAM event at DL – on Drishti / Avizo
>
>
  • CECAM event at DL – on Drishti / Avizo
 
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
Changed:
<
<
  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
>
>
 
  • EU COST grant: application for 2017

Proposals (speculative):

  • Link with Newton Fund (Global Challenge Research Fund) regarding STFC activities
Changed:
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<
  • Speculative with Innovate UK – Bill Lionheart
  • 3DSIM Inc – additive manufacturing contact (mathematical simulation)
  • Links with CFD groups – links and discussion with groups in UoM and STFC.
>
>
  • Speculative with Innovate UK – Bill Lionheart
  • 3DSIM Inc – additive manufacturing contact (mathematical simulation)
  • Links with CFD groups – links and discussion with groups in UoM and STFC.
  List of meetings:

  • EPSRC Software Strategy Workshop, 24 October 2016 in London
  • Working Group Meeting is booked for 21 November 2016: 10am-1pm. A possible speaker(s) is required.
Changed:
<
<
  • SHRI computational needs with Hartree – very speculative idea for cognitive / machine-learning needs from (mike.holmes at KTN); meeting at Imperial, 23 November 2016
>
>
  • SHRI computational needs with Hartree – very speculative idea for cognitive / machine-learning needs from (mike.holmes at KTN); meeting at Imperial, 23 November 2016
  Datasets:
Line: 1210 to 1226
 
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.

Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News

Changed:
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Appendix B – details of events June 2016-November 2016

>
>

Appendix B – details of events June 2016-November 2016

 

Three students over the summer

Changed:
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  1. One at RAL – sponsored by ULTRA/IMAT - Resulting in work for the IMAT launch event on 10 October 2016
  2. Two at UoM – sponsored by CCPi - Software development for reconstruction development
>
>
  1. One at RAL – sponsored by ULTRA/IMAT - Resulting in work for the IMAT launch event on 10 October 2016
  2. Two at UoM – sponsored by CCPi - Software development for reconstruction development
  Eight CCPi (Short-term) Fellows: most requested small travel funds.
Changed:
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  • 7 October 2016 Seminar. Lucia Mancini beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source
  • 8 September 2016; at RAL AND 12 September 2016 at University of Manchester - Visit by Marcus Hanwell (Kitware Inc) for tomviz.org product show-and-tell
  • "Fringe Meeting": Workshop @RAL on Advances in X-ray Imaging: Expanding the Frontiers of Knowledge 10 June 2016 Thilo Morgenmeyer, Mines ParisTech, France; Simon Jacques, UoM/UK Catalysis Hub; and Nikolay Osipov & Stephane Quilici , Mines ParisTech, France;
  • Round trip for 'hacking Nikon Metrology X-ray Custom bay": Southampton and RAL 8-9 June Parmesh Gajjar , University of Manchester
  • Extra: 8. - Impromptu presentation by visiting lecturer Dr Hamish Carr : May 2016 at RAL. Code for ContourTree manipulation for volumes to create multiple (level set type) isosurfaces.
>
>
  • 7 October 2016 Seminar. Lucia Mancini beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source
  • 8 September 2016; at RAL AND 12 September 2016 at University of Manchester - Visit by Marcus Hanwell (Kitware Inc) for tomviz.org product show-and-tell
  • "Fringe Meeting": Workshop @RAL on Advances in X-ray Imaging: Expanding the Frontiers of Knowledge 10 June 2016 Thilo Morgenmeyer, Mines ParisTech, France; Simon Jacques, UoM/UK Catalysis Hub; and Nikolay Osipov & Stephane Quilici , Mines ParisTech, France;
  • Round trip for 'hacking Nikon Metrology X-ray Custom bay": Southampton and RAL 8-9 June Parmesh Gajjar , University of Manchester
  • Extra: 8. - Impromptu presentation by visiting lecturer Dr Hamish Carr : May 2016 at RAL. Code for ContourTree manipulation for volumes to create multiple (level set type) isosurfaces.
  Seminars: Six seminars badged with CCPi logo
Changed:
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  • Seminar UoM - Lucia Mancini: 7 October (UoM)
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU: https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"
>
>
  • Seminar UoM - Lucia Mancini: 7 October (UoM)
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU:https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"
  Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Public Engagement; Five events:

Changed:
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  • RCaH's Royal Society exhibit travels to Manchester Science Festival for satellite exhibition on 24-28 October 2016
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
>
>
  • RCaH's Royal Society exhibit travels to Manchester Science Festival for satellite exhibition on 24-28 October 2016
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016
  Training ; six advertised:
Changed:
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  • FEI Visit and Workshop planned 24 November 2016 - Sri Nagella 12 attendees
  • Avizo courses 13 October 2016 Manchester-Noriko.Griffiths 20 places
  • Pre-ToScA Workshops on Monday 5th September 2016 at the University of Bath Avizo, VGStudio Max and Drishti. Full event with 38 attendees.
  • Avizo courses 16 to 18 August 2016 Manchester: Noriko.Griffiths@manchester.ac.uk 20 places
  • Hartree Summer School - Image Based Modelling examples were shown and described: 28 June 2016: one hour session in afternoon 12 attendees
  • 13 June 2016 Drishti workshop (HMXIF at Manchester, 8 attendees
  • 18 May 2016 HMXF Lunch and Learn and a follow on Training Session with Parmesh Gajjar on hacking the Nikon imaging devices (initially the custom bay units) 7 places .
>
>
  • FEI Visit and Workshop planned 24 November 2016 - Sri Nagella 12 attendees
  • Avizo courses 13 October 2016 Manchester-Noriko.Griffiths 20 places
  • Pre-ToScA Workshops on Monday 5th September 2016 at the University of Bath Avizo, VGStudio Max and Drishti. Full event with 38 attendees.
  • Avizo courses 16 to 18 August 2016 Manchester: Noriko.Griffiths@manchester.ac.uk 20 places
  • Hartree Summer School - Image Based Modelling examples were shown and described: 28 June 2016: one hour session in afternoon 12 attendees
  • 13 June 2016 Drishti workshop (HMXIF at Manchester, 8 attendees
  • 18 May 2016 HMXF Lunch and Learn and a follow on Training Session with Parmesh Gajjar on hacking the Nikon imaging devices (initially the custom bay units) 7 places .
  CCPi Publications:
Changed:
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  • 15-16 September EGUK CGVC - short paper on EPSRC SLA survey results for CCPs presented at Bournemouth.
  • CCPi related posters at ToScA include eight from partners:
    • Willliam Lionheart et al Exact and iterative helical scan reconstruction on the Nikon XTEK
    • Valeriy Titarenko et al Multi-source high speed scans of large objects with Rapiscan RTT 110
    • Mario Sandoval et al 6DoF Input Device Integration for XCT Volume Visualisation
    • Valeriy Titarenko et al Parallelising algorithms for x-ray tomography problems
    • Parmesh Gajjar et al Beyond a black box: 'Hacking' a Nion Metrology X-Ray CT Machine
    • James O'Sullivan et al Visualising the parasitic nematode Trichuris muris using X-ray micro-computed tomography
    • Dan Sykes et al Learning from nature: Time-lapse 3D imaging of the mechanical behaviour of arthropod cuticle
    • Biguri, Ander; Dosanjh, Manjit; Hancock, Steven; Soleimani, Manuchehr: TIGRE: Tomographic Iterative GPU-based Reconstruction toolbox
>
>
  • 15-16 September EGUK CGVC - short paper on EPSRC SLA survey results for CCPs presented at Bournemouth.
  • CCPi related posters at ToScA include eight from partners:
    • Willliam Lionheart et al Exact and iterative helical scan reconstruction on the Nikon XTEK
    • Valeriy Titarenko et al Multi-source high speed scans of large objects with Rapiscan RTT 110
    • Mario Sandoval et al 6DoF Input Device Integration for XCT Volume Visualisation
    • Valeriy Titarenko et al Parallelising algorithms for x-ray tomography problems
    • Parmesh Gajjar et al Beyond a black box: 'Hacking' a Nion Metrology X-Ray CT Machine
    • James O'Sullivan et al Visualising the parasitic nematode Trichuris muris using X-ray micro-computed tomography
    • Dan Sykes et al Learning from nature: Time-lapse 3D imaging of the mechanical behaviour of arthropod cuticle
    • Biguri, Ander; Dosanjh, Manjit; Hancock, Steven; Soleimani, Manuchehr: TIGRE: Tomographic Iterative GPU-based Reconstruction toolbox
  Extras:
Changed:
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  • Attended the 10 May 2016 Dimensional X-ray Computed Tomography Conference 2016 Venue: National Physical Laboratory Teddington UK.
>
>
  • Attended the 10 May 2016 Dimensional X-ray Computed Tomography Conference 2016 Venue: National Physical Laboratory Teddington UK.
  Email list ( CCPI-MEMBERS@JISCMAIL.AC.UK) has 314 subscribers; 40 new members since June 2016
Changed:
<
<
  1. shanshan.cheng@
  2. luke.rollings@
  3. joseph.monaghan@
  4. thomas.slater-2@
  5. g.poolo@
  6. tobias.starborg@
  7. jason.wild@
  8. A.Raviraj@
  9. Shashidhara.marathe@
  10. matthew.curd@
  11. ryanlloyd294@
  12. martyn.winn@
  13. chenwillcon@
  14. lucia.mancini@
  15. B.Winiarski@
  16. sarah-jane.clelland@
  17. thomas.sorensen@
  18. dan.sykes@
  19. yngve.m.moe@
  20. sara.nonni@
  21. steve.collins@
  22. paul.evans@
  23. ying.wang-4@
  24. thilo.morgeneyer@
  25. fabien.leonard@
  26. vitaliy.mykhaylyk@
  27. razvan.sencu@
  28. parmesh.gajjar@
  29. Noriko.Griffiths@
  30. genoveva.burca@
  31. Neil.Bourne@
  32. joe.kelleher@
  33. alun.ashton@
  34. evgueni.ovtchinnikov@
  35. jenny.woods@
  36. armin.wagner@
  37. alex.cl.leung@
  38. frank.von-delft@
  39. kamel.madi@
  40. wen.zhang-10@
>
>
  1. shanshan.cheng@
  2. luke.rollings@
  3. joseph.monaghan@
  4. thomas.slater-2@
  5. g.poolo@
  6. tobias.starborg@
  7. jason.wild@
  8. A.Raviraj@
  9. Shashidhara.marathe@
  10. matthew.curd@
  11. ryanlloyd294@
  12. martyn.winn@
  13. chenwillcon@
  14. lucia.mancini@
  15. B.Winiarski@
  16. sarah-jane.clelland@
  17. thomas.sorensen@
  18. dan.sykes@
  19. yngve.m.moe@
  20. sara.nonni@
  21. steve.collins@
  22. paul.evans@
  23. ying.wang-4@
  24. thilo.morgeneyer@
  25. fabien.leonard@
  26. vitaliy.mykhaylyk@
  27. razvan.sencu@
  28. parmesh.gajjar@
  29. Noriko.Griffiths@
  30. genoveva.burca@
  31. Neil.Bourne@
  32. joe.kelleher@
  33. alun.ashton@
  34. evgueni.ovtchinnikov@
  35. jenny.woods@
  36. armin.wagner@
  37. alex.cl.leung@
  38. frank.von-delft@
  39. kamel.madi@
  40. wen.zhang-10@
 

Roadmap and standards

Changed:
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Reminder and FYI the CCPi (tomographic Imaging) has a user list of about 330 people and slowly growing – and other community XCT lists exist; NPL’s and ToScA’s with NHM for example; so this is timely. My initial document from this proposal listed numerous technologies rising from the XCT development – that are beyond simple scale quantification; including (multi-scale) imaging analysis and other derived; chemistry, stress etc processes.
>
>
Reminder and FYI the CCPi (tomographic Imaging) has a user list of about 330 people and slowly growing – and other community XCT lists exist; NPL’s and ToScA ’s with NHM for example; so this is timely. My initial document from this proposal listed numerous technologies rising from the XCT development – that are beyond simple scale quantification; including (multi-scale) imaging analysis and other derived; chemistry, stress etc processes.
  I see two main outcomes in the UK;
Changed:
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  • 1. simpler imaging systems - similar to the development of SEM where cheaper lab based facilities with a kite-mark of standardisation are affordable to all groups (£<50K), and installed with Guides of Practice to 100's of groups within the UK from small university research labs to SME manufacturing facilities.
  • and 2. high-end very fast and multi-channel/energy imaging systems - creating large data deluge that allow multiple parameters to be recorded at once and continually giving physics, biology, chemistry and engineering values for sub/global-parts of an object under multitude types of influence (different environment in-situ rigs); changing temperature, pressure, shearing, catalytic reaction etc.
>
>
  • 1. simpler imaging systems - similar to the development of SEM where cheaper lab based facilities with a kite-mark of standardisation are affordable to all groups (£<50K), and installed with Guides of Practice to 100's of groups within the UK from small university research labs to SME manufacturing facilities.
  • and 2. high-end very fast and multi-channel/energy imaging systems - creating large data deluge that allow multiple parameters to be recorded at once and continually giving physics, biology, chemistry and engineering values for sub/global-parts of an object under multitude types of influence (different environment in-situ rigs); changing temperature, pressure, shearing, catalytic reaction etc.
 
Changed:
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So many places will have one or a few systems and some will have a multitude of systems – over many scales/ (in-situ)rigs / and all being 4D or 5D (temporal etc) and thus becoming bid data problems.
>
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So many places will have one or a few systems and some will have a multitude of systems – over many scales/ (in-situ)rigs / and all being 4D or 5D (temporal etc) and thus becoming bid data problems.
 

Line: 1434 to 1450
  2. Training and developer's days are to continue as normal
Changed:
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3. The next "away-day" developers’ day is proposed to be at the Warwick University Manufacturing group
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3. The next "away-day" developers’ day is proposed to be at the Warwick University Manufacturing group
  4. Future software show-and-tell events will be based on the suppliers and three Frameworks
Line: 1448 to 1464
  From the developers;' day (att 8). Code from STIR stir.soureforge.net STIR system needs updating - PET/SPECT code is available under the L esser GPL for libs: otherwise it is GPL but may move to Apache License. The size and performance is key with 600 x 60 rings giving 200-400m events resulting in a final volume size of about 200 cubed. Main issues are noise due to a lots of random events and scatter, about ¼ snr. Separate parts could be optimised/parallised; regulariser could be improved etc. constrained optimiser (LGFBF). Future work needs to consider:
Changed:
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  1. MPI/Open-MP/GPU (lots of race conditions)
  2. Matlab interface
  3. memory management to be improved esp for 3D data
  4. rotation based optimisation
>
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  1. MPI/Open-MP/GPU (lots of race conditions)
  2. Matlab interface
  3. memory management to be improved esp for 3D data
  4. rotation based optimisation
  Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
Line: 1476 to 1492
 

Items 2015-2016

Changed:
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  • 2 Feb - 1 May 2015: Visiting Scholar, Noicola Wadeson: signed contract
>
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  • 2 Feb - 1 May 2015: Visiting Scholar, Noicola Wadeson: signed contract
  Past CCPi activities: Compressed Sensing: funding from from Soton (Thomas Blumensath):
Line: 1506 to 1522
 
  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
Changed:
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  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel: http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
>
>
 
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.

Metrics 2013/4 need values for 2014/5

Changed:
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FOR ALL CCPs. We would highlight that during the financial year 2013/4 (figures from last year’s report in brackets):
>
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FOR ALL CCPs. We would highlight that during the financial year 2013/4 (figures from last year’s report in brackets):
 
Changed:
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  • STFC staff have produced some 51 (107) publications not including papers in preparation
  • STFC staff have given some 101 (109) presentations at meetings ranging from informal site visits to invited talks at major conferences.
  • There are some 1629 (1497) publications that reference codes developed through the SLA
  • Some 4451 (3732) training days covering !PhD supervision, code workshops and scientific meetings.
>
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  • STFC staff have produced some 51 (107) publications not including papers in preparation
  • STFC staff have given some 101 (109) presentations at meetings ranging from informal site visits to invited talks at major conferences.
  • There are some 1629 (1497) publications that reference codes developed through the SLA
  • Some 4451 (3732) training days covering PhD supervision, code workshops and scientific meetings.
  NEED metrics for CCPi.
Line: 1526 to 1542
 

Technical Appendix 2014 and plans for 2015

Changed:
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CCPi – Tomographic Imaging
>
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CCPi – Tomographic Imaging
  Non destructive 3D X-ray imaging is becoming increasingly important in many areas of science and its application to Energy, Healthcare and Security. For example it is having a dramatic impact on fields as diverse as security (e.g. baggage and body scanning at airports and screening of vehicles at ports), engineering (e.g. visualising stress corrosion cracking in nuclear plant and the degradation of fuel cells) and medicine (e.g. cancer treatment and artificial tissue engineering). The spatial and temporal resolutions are increasing dramatically. RC funded synchrotron sources are rapidly increasing the numbers of x-ray imaging instruments available (the European Synchrotron Radiation Facility (ESRF) now has 10 beamlines, Diamond Light Source (DLS) is currently building 4 new imaging beamlines). Laboratory x-ray imaging facilities are becoming increasingly widespread. This expansion is mirrored elsewhere with the global CT market now worth $150M (+ $5B in medical CT) both expanding at 10% pa , while 30% of the data stored on the world's computers are now medical images. Unsurprisingly, papers on x-ray tomography have also increased sharply this decade (doubling every 3 years with 1,500 published last year).
Line: 1536 to 1552
  Most people who acquire and analyse X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL will:
Changed:
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  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.
>
>
  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.
  This project aims to provide toolboxes for both 3D image reconstruction and 3D image analysis algorithms. In simple terms it is estimated that the project requires 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.

CCPi Milestone Date

Changed:
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  • 1 Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  • 2. Support current training courses and organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) - Q4 2014
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets
  • Extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as an option with DAWN - Q1 2015) Q4 2014
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images.
  • Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - (Release data release version Q1 2015) Q2 2014
  • 5. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, !ImageJ and !ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015
>
>
  • 1 Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  • 2. Support current training courses and organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) - Q4 2014
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets
  • Extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as an option with DAWN - Q1 2015) Q4 2014
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images.
  • Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - (Release data release version Q1 2015) Q2 2014
  • 5. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, ImageJ and ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015
  Task Effort Including Underspend
Changed:
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  • Additional Overall Coordination 0.2 (Turner)
  • Maintaining network, website, running workshops and training course, benchmarking, licencing issues 0.5
  • Developing and maintaining the 3D image analysis toolbox 0.5
  • Developing and maintaining the image reconstruction toolbox 0.5
  • Evaluation of neutron imaging software 0.25 (Yang)
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  • Additional Overall Coordination 0.2 (Turner)
  • Maintaining network, website, running workshops and training course, benchmarking, licencing issues 0.5
  • Developing and maintaining the 3D image analysis toolbox 0.5
  • Developing and maintaining the image reconstruction toolbox 0.5
  • Evaluation of neutron imaging software 0.25 (Yang)
  Total 1.5 FTEs carried ovcer underspend 0.45 FTE

Staffing Effort including Underspend

Changed:
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  • Martin Turner 0.2
  • Barry Searle 0.6
  • Srikanth Nagella 0.6
  • Ron Fowler 0.3
  • Erica Yang 0.25
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  • Martin Turner 0.2
  • Barry Searle 0.6
  • Srikanth Nagella 0.6
  • Ron Fowler 0.3
  • Erica Yang 0.25
  Total 1.5 + 0.45
Line: 1623 to 1639
  The last draft minutes are available at:
Changed:
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http://www.ccpi.ac.uk/minutes.shtml
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<a target="_blank" href="https://outlook.manchester.ac.uk/owa/redir.aspx?C=49cgmQyKAkCHhVVJOxUUZIEdDiT64NEITNzxDCPsrjr9UHYJ12AQ3Y-soR1eNwOOKgnjwaLDf5I.&URL=http%3a%2f%2fwww.ccpi.ac.uk%2fminutes.shtml" style="font-size: 10pt">http://www.ccpi.ac.uk/minutes.shtml</a>
 

CCPi Phase 2 Objectives

The new EPSRC proposal for CCPs is due on 7 October 2014 Key next stage progress items for the community are:

Changed:
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  • Include Neutron Tomography - link with ISIS IMAT bamline
  • Further close collaboration with DLS tomography and use outside of the national facilities
  • Code replacement for black-box reconstructions currently within lab based systems
  • Include Impedence Tomography - links also with ..
  • ... multimodality operations
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  • Include Neutron Tomography - link with ISIS IMAT bamline
  • Further close collaboration with DLS tomography and use outside of the national facilities
  • Code replacement for black-box reconstructions currently within lab based systems
  • Include Impedence Tomography - links also with ..
  • ... multimodality operations
  Increase use and functionality of the reconstrcution and quantification toolkits currently available. Consider further dataflow and linking together tools.

ACTIONS We need to submit to SCD (STFC) [to discuss with Paul Sherwood] an outline workplan - one page or two: IN TWO WEEKS TIME (19 September 2014)

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  • What code needs to be defined / updated
  • Very general milestones - covering mainly first year of the five year plan
  • Amount of SLA support requested - could expand from 1.5FTE to 2.0FTE
  • Type of support - can state need experience / links to facilities
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  • What code needs to be defined / updated
  • Very general milestones - covering mainly first year of the five year plan
  • Amount of SLA support requested - could expand from 1.5FTE to 2.0FTE
  • Type of support - can state need experience / links to facilities
  ACTIONS Final submission is only one JeS for the CCPi Mark2 - DUE 7 OCTOBER 2014
Line: 1656 to 1672
  Most people who acquire and analyse X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL will:
Changed:
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  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.
>
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  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.
  This project aims to provide toolboxes for both 3D image reconstruction and 3D image analysis algorithms. In simple terms it is estimated that the project requires 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.
Line: 1682 to 1698
  Development targets met:
Changed:
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  1. Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  2. We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  3. Iterative reconstruction development proceeds; we have completed a !NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre !ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
  4. The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
  5. Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  6. Optimise projection algorithm at core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  7. Add 2 new iterative reconstruction algorithms from network members or flagship project to reconstruction suite Q1 2014. at a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the ccpforge archive and a way forwrd is being used.
>
>
  1. Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  2. We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  3. Iterative reconstruction development proceeds; we have completed a NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
  4. The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel " target="_blank">http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ]]
  5. Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  6. Optimise projection algorithm at core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  7. Add 2 new iterative reconstruction algorithms from network members or flagship project to reconstruction suite Q1 2014. at a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the ccpforge archive and a way forwrd is being used.
  Deliverables produced:
Changed:
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
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Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004
 
Changed:
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“4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
>
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“4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and
 
Changed:
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“Multimodal image reconstruction using supplementary structural information in total variation regularization” on second revision in “Sensing and Imaging”.
>
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“Multimodal image reconstruction using supplementary structural information in total variation regularization” on second revision in “Sensing and Imaging”.
  Presentations: Last year there have been;
Changed:
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  • Monthly software show-and-tell events from August 2013 - March 2014: eight meetings (total attendance, 113)
  • The first Software Developers' Workshops with presentations and discussions (14 January 2014 Developers' day at Birmingham; attend 14)
  • Stand at Materials KTN Materials Research Exchange (24-)25 February 2014, Ricoh Arena, Coventry. This promoted the HIP, CCPi, Hartee Centre and related facilities including ISIS. There was also a one-minute pitch "The Use of Synchrotron and Neutron Imaging within Materials Science using STFC Facilities"
  • Combined stand for CCPi and HIP at the IIP 6 November 2013. Included pull-up stand, case studies and a poster for the main CCPi activities.
>
>
  • Monthly software show-and-tell events from August 2013 - March 2014: eight meetings (total attendance, 113)
  • The first Software Developers' Workshops with presentations and discussions (14 January 2014 Developers' day at Birmingham; attend 14)
  • Stand at Materials KTN Materials Research Exchange (24-)25 February 2014, Ricoh Arena, Coventry. This promoted the HIP, CCPi, Hartee Centre and related facilities including ISIS. There was also a one-minute pitch "The Use of Synchrotron and Neutron Imaging within Materials Science using STFC Facilities"
  • Combined stand for CCPi and HIP at the IIP 6 November 2013. Included pull-up stand, case studies and a poster for the main CCPi activities.
  Training sessions: Across Diamond / RCaH / University of Manchester Collaboration / STFC labs there have been 9 training courses (total attendance; 117) .
Changed:
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  • Diamond [Approx 26+19 (about 30 PhD)] 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data; 15-17 January 2014 Avizo and CT course DLS/STFC
  • UoM [Approx 10+9] 28-29 January 2014 Avizo and CT; 29 October - 1 November 2013, Avizo and CT
  • RCaH [Approx 8+22+7+7] 27-28 January 2014 RCaH Training Course in CT and Avizo; - 9th July 2013 Manchester CT reconstruction at Diamond workshop; 7-8 October 2013, Avizo (VSG) and 12 December DVC training course by RCaH at RAL
  • RAL [Approx 9] 24-26 June 2013, Avizo (VSG)
>
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  • Diamond [Approx 26+19 (about 30 PhD)] 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data; 15-17 January 2014 Avizo and CT course DLS/STFC
  • UoM [Approx 10+9] 28-29 January 2014 Avizo and CT; 29 October - 1 November 2013, Avizo and CT
  • RCaH [Approx 8+22+7+7] 27-28 January 2014 RCaH Training Course in CT and Avizo; - 9th July 2013 Manchester CT reconstruction at Diamond workshop; 7-8 October 2013, Avizo (VSG) and 12 December DVC training course by RCaH at RAL
  • RAL [Approx 9] 24-26 June 2013, Avizo (VSG)
 
Line: 1718 to 1734
 
  1. Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  2. Support current training courses and organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) - Q4 2014
Changed:
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  1. Port 3 or 4 iterative codes so that they can be compared on the same datasets - Q4 2014 (extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS package as anoption with DAWN - Q1 2015)
  2. Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - Q2 2014 (Release data release version Q1 2015)
  3. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 -Q3 2014
  4. Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, !ImageJ and !ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
>
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  1. Port 3 or 4 iterative codes so that they can be compared on the same datasets - Q4 2014 (extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS package as anoption with DAWN - Q1 2015)
  2. Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - Q2 2014 (Release data release version Q1 2015)
  3. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 -Q3 2014
  4. Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, ImageJ and ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
  Extra Admin target to promote once complete as is in progress at Manchester with the lab based systems.
Changed:
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  1. Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
>
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  1. Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
 
Line: 1740 to 1756
  Items from discussion:
Changed:
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  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
  • Manchester/Diamond code - modified for cone-beam reconstruction.
  • Used code for images with a missing wedge - there is new in situ kit that will have some blind views.
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets. October 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) July 2014
>
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  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
  • Manchester/Diamond code - modified for cone-beam reconstruction.
  • Used code for images with a missing wedge - there is new in situ kit that will have some blind views.
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets. October 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) July 2014
 

Extra Activities

Line: 1768 to 1784
  Items from discussion:
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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
  • Algorithms awaiting publication: support to be given.
  • Potential to support Avizo, ImageJ and ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms. Novemeber 2014
  • Develop a project to re-engineer an existing code for Digital Image Correlation. Q2 2014 (Work with Brian Bay (the original developer) of Oregon State University; This would be a plug-in to Avizo and ImageJ, something novel to both applications)
>
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  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
  • Algorithms awaiting publication: support to be given.
  • Potential to support Avizo, ImageJ and ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms. Novemeber 2014
  • Develop a project to re-engineer an existing code for Digital Image Correlation. Q2 2014 (Work with Brian Bay (the original developer) of Oregon State University; This would be a plug-in to Avizo and ImageJ, something novel to both applications)
 

Extra training:

Changed:
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  • Continue support for CCPi training courses given by community
  • Organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) December 2014
>
>
  • Continue support for CCPi training courses given by community
  • Organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) December 2014
  Extra Activities
Line: 1788 to 1804
  Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.
Changed:
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
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A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf
  - Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).
Changed:
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Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
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Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".
 

Administration Items

Items to be acted upon - as well as meetings and training as below.

Changed:
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  • CECAM conference/workshop (possibly synergistic with COST Extrema)
  • Phil Trans Special Issue Mark 1
  • Support for CCP4Vis and future CCPi mark 2
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  • CECAM conference/workshop (possibly synergistic with COST Extrema)
  • Phil Trans Special Issue Mark 1
  • Support for CCP4Vis and future CCPi mark 2
 
  • Interim report in October on all CCPi targets
  • CCPi survey dissemination and use cases
  • ...

Papers etc.:

Changed:
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
>
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  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)
  Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.
Line: 1815 to 1831
  There is a Core 0.5 FTE management time available to support activities and manage listserv's etc.
Changed:
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  • Tuesday 20 May 2014 - CCPi software developers' day in Birmingham - focus of this is on reconstruction algorithms with an emphasis on DLS and the DAWN system
  • Wednesday 21 May 2014 - Celebration of Queen's Anniversary Prize for New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries , University of Manchester: 22 May
  • Friday 30 May 2014 - Tomo-and-Coffee session: proposed "dataflow session using volume vis in paraview" (RAL, 2pm)
  • Tuesday 10 June 2014 - CCP Steering Panel - only CCPi PI attending, Phil Withers, but we may need to feed details for the report into this.
  • Monday 17 June 2014 - CCPi Working Group meeting - either at RAL or DL. 6-monthly meeting.
  • Thursday 27 June 2014 - DLS reviewing their dataflow system DAWN on the RAL Tomo-and-Coffee session (2pm)
  • 22 July 2014 - CCPi software developers' day in Nottingham - visit to the new Hounsfield facility. Date to be confirmed.
  • 1-3 September 2014 - CCPi co-sponsoring, Tomography for Scientific Advancement (ToScA) Symposium in affiliation with the Royal Microscopy Society at the Natural History Museum, London, UK
  • Sponsoring through HIP: Young Researchers in Image-based Modelling 9 September 2014.
>
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  • Tuesday 20 May 2014 - CCPi software developers' day in Birmingham - focus of this is on reconstruction algorithms with an emphasis on DLS and the DAWN system
  • Wednesday 21 May 2014 - Celebration of Queen's Anniversary Prize for New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries , University of Manchester: 22 May
  • Friday 30 May 2014 - Tomo-and-Coffee session: proposed "dataflow session using volume vis in paraview" (RAL, 2pm)
  • Tuesday 10 June 2014 - CCP Steering Panel - only CCPi PI attending, Phil Withers, but we may need to feed details for the report into this.
  • Monday 17 June 2014 - CCPi Working Group meeting - either at RAL or DL. 6-monthly meeting.
  • Thursday 27 June 2014 - DLS reviewing their dataflow system DAWN on the RAL Tomo-and-Coffee session (2pm)
  • 22 July 2014 - CCPi software developers' day in Nottingham - visit to the new Hounsfield facility. Date to be confirmed.
  • 1-3 September 2014 - CCPi co-sponsoring, Tomography for Scientific Advancement (ToScA) Symposium in